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/7915867/working' mkdir: created directory `/scratch/stefan/7915867/working/protonate' Storing results in /scratch/stefan/7915867/finished Working in /scratch/stefan/7915867/working /scratch/stefan/7915867/working /scratch/stefan/7915867 /scratch/stefan/7915867/working/protonate /scratch/stefan/7915867/working /scratch/stefan/7915867 Precomputing protomers for all compounds (pH: 7.4) awk: cmd. line:1: fatal: cannot open file `/nfs/home/stefan/.install4j' for reading (No such file or directory) rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory rm: cannot remove `/nfs/home/stefan/.install4j': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory mv: cannot stat `/nfs/home/stefan/.install4j_new': No such file or directory ph 7.4: 48 protomers created Coalesing and merging protomers 48 protomers generated for 48 compounds Checking for new stereocenters and expanding 48 protomers after new stereo-center expansion /scratch/stefan/7915867/working /scratch/stefan/7915867 Bulk generating 3D conformations all protomers in /scratch/stefan/7915867/working/3D mkdir: created directory `/scratch/stefan/7915867/working/3D' We are using corina for 3D embeding debuging info:: /scratch/stefan/7915867/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' 49 3D conformations generated for 48 compounds Building REAL250005014383 mkdir: created directory `/scratch/stefan/7915867/working/building' mkdir: created directory `/scratch/stefan/7915867/working/building/REAL250005014383' /scratch/stefan/7915867/working/building/REAL250005014383 /scratch/stefan/7915867/working /scratch/stefan/7915867 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005014383 mkdir: created directory `0' /scratch/stefan/7915867/working/building/REAL250005014383/0 /scratch/stefan/7915867/working/building/REAL250005014383 /scratch/stefan/7915867/working /scratch/stefan/7915867 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/stefan/7915867/working/3D/1 `/scratch/stefan/7915867/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CNS(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-]) `REAL250005014383.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005014383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7915867/working/building/REAL250005014383/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014383 none CC(C)CNS(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [29, 26, 33, 11, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 33, 26, 26, 11, 1, 1] 33 rigid atoms, others: [5, 8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28] set([0, 1, 2, 3, 4, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7915867/working/building/REAL250005014383 /scratch/stefan/7915867/working /scratch/stefan/7915867 Finished preparing REAL250005014383 Recording results /scratch/stefan/7915867/working /scratch/stefan/7915867 mkdir: created directory `/scratch/stefan/7915867/finished' Appending to /scratch/stefan/7915867/finished/xaaaaaa.* 0: /scratch/stefan/7915867/working/building/REAL250005014383/0.* Removing working files in /scratch/stefan/7915867/working/building/REAL250005014383 Building REAL250005014384 mkdir: created directory `/scratch/stefan/7915867/working/building/REAL250005014384' /scratch/stefan/7915867/working/building/REAL250005014384 /scratch/stefan/7915867/working /scratch/stefan/7915867 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005014384 mkdir: created directory `0' /scratch/stefan/7915867/working/building/REAL250005014384/0 /scratch/stefan/7915867/working/building/REAL250005014384 /scratch/stefan/7915867/working /scratch/stefan/7915867 Protomer 0 (index: 2) Found valid previously generated 3D confromation in /scratch/stefan/7915867/working/3D/2 `/scratch/stefan/7915867/working/3D/2' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)N(C)S(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-]) `REAL250005014384.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005014384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7915867/working/building/REAL250005014384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014384 none CC(C)N(C)S(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 14, 11, 11, 1, 1, 1, 16, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1] 15 rigid atoms, others: [5, 8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28] set([0, 1, 2, 3, 4, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7915867/working/building/REAL250005014384 /scratch/stefan/7915867/working /scratch/stefan/7915867 Finished preparing REAL250005014384 Recording results /scratch/stefan/7915867/working /scratch/stefan/7915867 Appending to /scratch/stefan/7915867/finished/xaaaaaa.* 0: /scratch/stefan/7915867/working/building/REAL250005014384/0.* Removing working files in /scratch/stefan/7915867/working/building/REAL250005014384 Building REAL250005014385 mkdir: created directory `/scratch/stefan/7915867/working/building/REAL250005014385' /scratch/stefan/7915867/working/building/REAL250005014385 /scratch/stefan/7915867/working /scratch/stefan/7915867 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005014385 mkdir: created directory `0' /scratch/stefan/7915867/working/building/REAL250005014385/0 /scratch/stefan/7915867/working/building/REAL250005014385 /scratch/stefan/7915867/working /scratch/stefan/7915867 Protomer 0 (index: 3) Found valid previously generated 3D confromation in /scratch/stefan/7915867/working/3D/3 `/scratch/stefan/7915867/working/3D/3' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCNS(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-]) `REAL250005014385.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005014385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7915867/working/building/REAL250005014385/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014385 none C#CCNS(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-] NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 16, 1, 12, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 9, 1, 1] 17 rigid atoms, others: [4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21] set([0, 1, 2, 3, 5, 6, 16, 17, 18, 19]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7915867/working/building/REAL250005014385 /scratch/stefan/7915867/working /scratch/stefan/7915867 Finished preparing REAL250005014385 Recording results /scratch/stefan/7915867/working /scratch/stefan/7915867 Appending to /scratch/stefan/7915867/finished/xaaaaaa.* 0: /scratch/stefan/7915867/working/building/REAL250005014385/0.* Removing working files in /scratch/stefan/7915867/working/building/REAL250005014385 Building REAL250005014386 mkdir: created directory `/scratch/stefan/7915867/working/building/REAL250005014386' /scratch/stefan/7915867/working/building/REAL250005014386 /scratch/stefan/7915867/working /scratch/stefan/7915867 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005014386 mkdir: created directory `0' /scratch/stefan/7915867/working/building/REAL250005014386/0 /scratch/stefan/7915867/working/building/REAL250005014386 /scratch/stefan/7915867/working /scratch/stefan/7915867 Protomer 0 (index: 4) Found valid previously generated 3D confromation in /scratch/stefan/7915867/working/3D/4 `/scratch/stefan/7915867/working/3D/4' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)NS(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-]) `REAL250005014386.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005014386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7915867/working/building/REAL250005014386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014386 none CCC(C)NS(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 14, 9, 14, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 14, 14, 14, 14, 9, 1, 1] 19 rigid atoms, others: [5, 8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28] set([0, 1, 2, 3, 4, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 82 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7915867/working/building/REAL250005014386 /scratch/stefan/7915867/working /scratch/stefan/7915867 Finished preparing REAL250005014386 Recording results /scratch/stefan/7915867/working /scratch/stefan/7915867 Appending to /scratch/stefan/7915867/finished/xaaaaaa.* 0: /scratch/stefan/7915867/working/building/REAL250005014386/0.* Removing working files in /scratch/stefan/7915867/working/building/REAL250005014386 Building REAL250005014387 mkdir: created directory `/scratch/stefan/7915867/working/building/REAL250005014387' /scratch/stefan/7915867/working/building/REAL250005014387 /scratch/stefan/7915867/working /scratch/stefan/7915867 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005014387 mkdir: created directory `0' /scratch/stefan/7915867/working/building/REAL250005014387/0 /scratch/stefan/7915867/working/building/REAL250005014387 /scratch/stefan/7915867/working /scratch/stefan/7915867 Protomer 0 (index: 5) Found valid previously generated 3D confromation in /scratch/stefan/7915867/working/3D/5 `/scratch/stefan/7915867/working/3D/5' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=S(=O)(C1=CC(Cl)=CC(Cl)=C1[O-])N1CCCC1) `REAL250005014387.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005014387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7915867/working/building/REAL250005014387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014387 none O=S(=O)(C1=CC(Cl)=CC(Cl)=C1[O-])N1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'S.o2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 14, 11, 1, 1, 1, 16, 1, 1, 16, 1, 12, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 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 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6] 6 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18] set([0, 2, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 19 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014387 none O=S(=O)(C1=CC(Cl)=CC(Cl)=C1[O-])N1CCCC1 NO_LONG_NAME dock atom types: ['O.2', 'S.o2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 14, 11, 1, 1, 1, 16, 1, 1, 16, 1, 12, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 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 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 6, 6, 6, 5, 6, 6, 6, 6, 1, 1, 1, 1, 1, 6, 5, 1, 1, 1, 1, 1, 1, 1, 1] 6 rigid atoms, others: [1, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18]) total number of confs: 21 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7915867/working/building/REAL250005014387 /scratch/stefan/7915867/working /scratch/stefan/7915867 Finished preparing REAL250005014387 Recording results /scratch/stefan/7915867/working /scratch/stefan/7915867 Appending to /scratch/stefan/7915867/finished/xaaaaaa.* 0: /scratch/stefan/7915867/working/building/REAL250005014387/0.* Removing working files in /scratch/stefan/7915867/working/building/REAL250005014387 Building REAL250005014388 mkdir: created directory `/scratch/stefan/7915867/working/building/REAL250005014388' /scratch/stefan/7915867/working/building/REAL250005014388 /scratch/stefan/7915867/working /scratch/stefan/7915867 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005014388 mkdir: created directory `0' /scratch/stefan/7915867/working/building/REAL250005014388/0 /scratch/stefan/7915867/working/building/REAL250005014388 /scratch/stefan/7915867/working /scratch/stefan/7915867 Protomer 0 (index: 6) Found valid previously generated 3D confromation in /scratch/stefan/7915867/working/3D/6 `/scratch/stefan/7915867/working/3D/6' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)S(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-]) `REAL250005014388.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005014388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7915867/working/building/REAL250005014388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014388 none CN(C)S(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 14, 11, 11, 1, 1, 1, 16, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 1, 1] 7 rigid atoms, others: [3, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 4, 5, 15, 16, 17, 18, 19, 20]) total number of confs: 22 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7915867/working/building/REAL250005014388 /scratch/stefan/7915867/working /scratch/stefan/7915867 Finished preparing REAL250005014388 Recording results /scratch/stefan/7915867/working /scratch/stefan/7915867 Appending to /scratch/stefan/7915867/finished/xaaaaaa.* 0: /scratch/stefan/7915867/working/building/REAL250005014388/0.* Removing working files in /scratch/stefan/7915867/working/building/REAL250005014388 Building REAL250005014389 mkdir: created directory `/scratch/stefan/7915867/working/building/REAL250005014389' /scratch/stefan/7915867/working/building/REAL250005014389 /scratch/stefan/7915867/working /scratch/stefan/7915867 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005014389 mkdir: created directory `0' /scratch/stefan/7915867/working/building/REAL250005014389/0 /scratch/stefan/7915867/working/building/REAL250005014389 /scratch/stefan/7915867/working /scratch/stefan/7915867 Protomer 0 (index: 7) Found valid previously generated 3D confromation in /scratch/stefan/7915867/working/3D/7 `/scratch/stefan/7915867/working/3D/7' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNS(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-]) `REAL250005014389.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005014389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7915867/working/building/REAL250005014389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014389 none CCNS(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 5, 1, 1] 7 rigid atoms, others: [3, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 4, 5, 15, 16, 17, 18, 19, 20]) total number of confs: 30 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7915867/working/building/REAL250005014389 /scratch/stefan/7915867/working /scratch/stefan/7915867 Finished preparing REAL250005014389 Recording results /scratch/stefan/7915867/working /scratch/stefan/7915867 Appending to /scratch/stefan/7915867/finished/xaaaaaa.* 0: /scratch/stefan/7915867/working/building/REAL250005014389/0.* Removing working files in /scratch/stefan/7915867/working/building/REAL250005014389 Building REAL250005014390 mkdir: created directory `/scratch/stefan/7915867/working/building/REAL250005014390' /scratch/stefan/7915867/working/building/REAL250005014390 /scratch/stefan/7915867/working /scratch/stefan/7915867 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005014390 mkdir: created directory `0' /scratch/stefan/7915867/working/building/REAL250005014390/0 /scratch/stefan/7915867/working/building/REAL250005014390 /scratch/stefan/7915867/working /scratch/stefan/7915867 Protomer 0 (index: 8) Found valid previously generated 3D confromation in /scratch/stefan/7915867/working/3D/8 `/scratch/stefan/7915867/working/3D/8' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNS(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-]) `REAL250005014390.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005014390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7915867/working/building/REAL250005014390/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014390 none CCCNS(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [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] 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, 27, 11, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 27, 27, 11, 1, 1] 37 rigid atoms, others: [4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25] set([0, 1, 2, 3, 5, 6, 16, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7915867/working/building/REAL250005014390 /scratch/stefan/7915867/working /scratch/stefan/7915867 Finished preparing REAL250005014390 Recording results /scratch/stefan/7915867/working /scratch/stefan/7915867 Appending to /scratch/stefan/7915867/finished/xaaaaaa.* 0: /scratch/stefan/7915867/working/building/REAL250005014390/0.* Removing working files in /scratch/stefan/7915867/working/building/REAL250005014390 Building REAL250005014391 mkdir: created directory `/scratch/stefan/7915867/working/building/REAL250005014391' /scratch/stefan/7915867/working/building/REAL250005014391 /scratch/stefan/7915867/working /scratch/stefan/7915867 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005014391 mkdir: created directory `0' /scratch/stefan/7915867/working/building/REAL250005014391/0 /scratch/stefan/7915867/working/building/REAL250005014391 /scratch/stefan/7915867/working /scratch/stefan/7915867 Protomer 0 (index: 9) Found valid previously generated 3D confromation in /scratch/stefan/7915867/working/3D/9 `/scratch/stefan/7915867/working/3D/9' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCNS(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-]) `REAL250005014391.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005014391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7915867/working/building/REAL250005014391/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014391 none C=CCNS(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-] NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 25, 13, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 25, 25, 13, 1, 1] 27 rigid atoms, others: [4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 5, 6, 16, 17, 18, 19, 20, 21]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7915867/working/building/REAL250005014391 /scratch/stefan/7915867/working /scratch/stefan/7915867 Finished preparing REAL250005014391 Recording results /scratch/stefan/7915867/working /scratch/stefan/7915867 Appending to /scratch/stefan/7915867/finished/xaaaaaa.* 0: /scratch/stefan/7915867/working/building/REAL250005014391/0.* Removing working files in /scratch/stefan/7915867/working/building/REAL250005014391 Building REAL250005014392 mkdir: created directory `/scratch/stefan/7915867/working/building/REAL250005014392' /scratch/stefan/7915867/working/building/REAL250005014392 /scratch/stefan/7915867/working /scratch/stefan/7915867 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005014392 mkdir: created directory `0' /scratch/stefan/7915867/working/building/REAL250005014392/0 /scratch/stefan/7915867/working/building/REAL250005014392 /scratch/stefan/7915867/working /scratch/stefan/7915867 Protomer 0 (index: 10) Found valid previously generated 3D confromation in /scratch/stefan/7915867/working/3D/10 `/scratch/stefan/7915867/working/3D/10' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)S(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-]) `REAL250005014392.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005014392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7915867/working/building/REAL250005014392/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014392 none CCN(CC)S(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 14, 11, 11, 1, 1, 1, 16, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 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: [22, 13, 7, 13, 20, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 20, 20, 20, 20, 20, 1, 1] 27 rigid atoms, others: [5, 8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28] set([0, 1, 2, 3, 4, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 136 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7915867/working/building/REAL250005014392 /scratch/stefan/7915867/working /scratch/stefan/7915867 Finished preparing REAL250005014392 Recording results /scratch/stefan/7915867/working /scratch/stefan/7915867 Appending to /scratch/stefan/7915867/finished/xaaaaaa.* 0: /scratch/stefan/7915867/working/building/REAL250005014392/0.* Removing working files in /scratch/stefan/7915867/working/building/REAL250005014392 Building REAL250005014393 mkdir: created directory `/scratch/stefan/7915867/working/building/REAL250005014393' /scratch/stefan/7915867/working/building/REAL250005014393 /scratch/stefan/7915867/working /scratch/stefan/7915867 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005014393 mkdir: created directory `0' /scratch/stefan/7915867/working/building/REAL250005014393/0 /scratch/stefan/7915867/working/building/REAL250005014393 /scratch/stefan/7915867/working /scratch/stefan/7915867 Protomer 0 (index: 11) Found valid previously generated 3D confromation in /scratch/stefan/7915867/working/3D/11 `/scratch/stefan/7915867/working/3D/11' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCCNS(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-]) `REAL250005014393.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005014393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7915867/working/building/REAL250005014393/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014393 none CCCCNS(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 51, 31, 13, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 73, 73, 73, 73, 73, 51, 51, 31, 31, 13, 1, 1] 73 rigid atoms, others: [5, 8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28] set([0, 1, 2, 3, 4, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 358 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7915867/working/building/REAL250005014393 /scratch/stefan/7915867/working /scratch/stefan/7915867 Finished preparing REAL250005014393 Recording results /scratch/stefan/7915867/working /scratch/stefan/7915867 Appending to /scratch/stefan/7915867/finished/xaaaaaa.* 0: /scratch/stefan/7915867/working/building/REAL250005014393/0.* Removing working files in /scratch/stefan/7915867/working/building/REAL250005014393 Building REAL250005014394 mkdir: created directory `/scratch/stefan/7915867/working/building/REAL250005014394' /scratch/stefan/7915867/working/building/REAL250005014394 /scratch/stefan/7915867/working /scratch/stefan/7915867 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005014394 mkdir: created directory `0' /scratch/stefan/7915867/working/building/REAL250005014394/0 /scratch/stefan/7915867/working/building/REAL250005014394 /scratch/stefan/7915867/working /scratch/stefan/7915867 Protomer 0 (index: 12) Found valid previously generated 3D confromation in /scratch/stefan/7915867/working/3D/12 `/scratch/stefan/7915867/working/3D/12' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)NS(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-]) `REAL250005014394.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005014394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7915867/working/building/REAL250005014394/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014394 none CC(C)NS(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [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] 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, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1] 11 rigid atoms, others: [4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25] set([0, 1, 2, 3, 5, 6, 16, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7915867/working/building/REAL250005014394 /scratch/stefan/7915867/working /scratch/stefan/7915867 Finished preparing REAL250005014394 Recording results /scratch/stefan/7915867/working /scratch/stefan/7915867 Appending to /scratch/stefan/7915867/finished/xaaaaaa.* 0: /scratch/stefan/7915867/working/building/REAL250005014394/0.* Removing working files in /scratch/stefan/7915867/working/building/REAL250005014394 Building REAL250005014395 mkdir: created directory `/scratch/stefan/7915867/working/building/REAL250005014395' /scratch/stefan/7915867/working/building/REAL250005014395 /scratch/stefan/7915867/working /scratch/stefan/7915867 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005014395 mkdir: created directory `0' /scratch/stefan/7915867/working/building/REAL250005014395/0 /scratch/stefan/7915867/working/building/REAL250005014395 /scratch/stefan/7915867/working /scratch/stefan/7915867 Protomer 0 (index: 13) Found valid previously generated 3D confromation in /scratch/stefan/7915867/working/3D/13 `/scratch/stefan/7915867/working/3D/13' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CON(C)S(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-]) `REAL250005014395.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005014395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7915867/working/building/REAL250005014395/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014395 none CON(C)S(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 8, 5, 14, 11, 11, 1, 1, 1, 16, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 5, 7, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 7, 7, 7, 1, 1] 11 rigid atoms, others: [4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23] set([0, 1, 2, 3, 5, 6, 16, 17, 18, 19, 20, 21]) total number of confs: 32 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7915867/working/building/REAL250005014395 /scratch/stefan/7915867/working /scratch/stefan/7915867 Finished preparing REAL250005014395 Recording results /scratch/stefan/7915867/working /scratch/stefan/7915867 Appending to /scratch/stefan/7915867/finished/xaaaaaa.* 0: /scratch/stefan/7915867/working/building/REAL250005014395/0.* Removing working files in /scratch/stefan/7915867/working/building/REAL250005014395 Building REAL250005014396 mkdir: created directory `/scratch/stefan/7915867/working/building/REAL250005014396' /scratch/stefan/7915867/working/building/REAL250005014396 /scratch/stefan/7915867/working /scratch/stefan/7915867 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005014396 mkdir: created directory `0' /scratch/stefan/7915867/working/building/REAL250005014396/0 /scratch/stefan/7915867/working/building/REAL250005014396 /scratch/stefan/7915867/working /scratch/stefan/7915867 Protomer 0 (index: 14) Found valid previously generated 3D confromation in /scratch/stefan/7915867/working/3D/14 `/scratch/stefan/7915867/working/3D/14' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNS(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-]) `REAL250005014396.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005014396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7915867/working/building/REAL250005014396/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014396 none CNS(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 16, 1, 12, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1] 5 rigid atoms, others: [2, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19] set([0, 1, 3, 4, 14, 15, 16, 17]) total number of confs: 18 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7915867/working/building/REAL250005014396 /scratch/stefan/7915867/working /scratch/stefan/7915867 Finished preparing REAL250005014396 Recording results /scratch/stefan/7915867/working /scratch/stefan/7915867 Appending to /scratch/stefan/7915867/finished/xaaaaaa.* 0: /scratch/stefan/7915867/working/building/REAL250005014396/0.* Removing working files in /scratch/stefan/7915867/working/building/REAL250005014396 Building REAL250005014397 mkdir: created directory `/scratch/stefan/7915867/working/building/REAL250005014397' /scratch/stefan/7915867/working/building/REAL250005014397 /scratch/stefan/7915867/working /scratch/stefan/7915867 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005014397 mkdir: created directory `0' /scratch/stefan/7915867/working/building/REAL250005014397/0 /scratch/stefan/7915867/working/building/REAL250005014397 /scratch/stefan/7915867/working /scratch/stefan/7915867 Protomer 0 (index: 15) Found valid previously generated 3D confromation in /scratch/stefan/7915867/working/3D/15 `/scratch/stefan/7915867/working/3D/15' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=S(=O)(NCC1CC1)C1=CC(Cl)=CC(Cl)=C1[O-]) `REAL250005014397.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005014397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7915867/working/building/REAL250005014397/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014397 none O=S(=O)(NCC1CC1)C1=CC(Cl)=CC(Cl)=C1[O-] NO_LONG_NAME dock atom types: ['O.2', 'S.o2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 14, 11, 8, 5, 5, 5, 5, 1, 1, 1, 16, 1, 1, 16, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [39, 24, 39, 8, 1, 1, 1, 1, 39, 41, 41, 41, 41, 41, 41, 41, 41, 24, 8, 8, 1, 1, 1, 1, 1, 41, 41] 41 rigid atoms, others: [4, 5, 6, 7, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26]) total number of confs: 152 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014397 none O=S(=O)(NCC1CC1)C1=CC(Cl)=CC(Cl)=C1[O-] NO_LONG_NAME dock atom types: ['O.2', 'S.o2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 14, 11, 8, 5, 5, 5, 5, 1, 1, 1, 16, 1, 1, 16, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 12, 32, 41, 41, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 32, 32, 41, 41, 41, 41, 41, 1, 1] 41 rigid atoms, others: [1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 154 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7915867/working/building/REAL250005014397 /scratch/stefan/7915867/working /scratch/stefan/7915867 Finished preparing REAL250005014397 Recording results /scratch/stefan/7915867/working /scratch/stefan/7915867 Appending to /scratch/stefan/7915867/finished/xaaaaaa.* 0: /scratch/stefan/7915867/working/building/REAL250005014397/0.* Removing working files in /scratch/stefan/7915867/working/building/REAL250005014397 Building REAL250005014398 mkdir: created directory `/scratch/stefan/7915867/working/building/REAL250005014398' /scratch/stefan/7915867/working/building/REAL250005014398 /scratch/stefan/7915867/working /scratch/stefan/7915867 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005014398 mkdir: created directory `0' /scratch/stefan/7915867/working/building/REAL250005014398/0 /scratch/stefan/7915867/working/building/REAL250005014398 /scratch/stefan/7915867/working /scratch/stefan/7915867 Protomer 0 (index: 16) Found valid previously generated 3D confromation in /scratch/stefan/7915867/working/3D/16 `/scratch/stefan/7915867/working/3D/16' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)S(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-]) `REAL250005014398.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005014398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7915867/working/building/REAL250005014398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014398 none CN(C)S(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 14, 11, 11, 1, 1, 1, 16, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 1, 1] 7 rigid atoms, others: [3, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 4, 5, 15, 16, 17, 18, 19, 20]) total number of confs: 22 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7915867/working/building/REAL250005014398 /scratch/stefan/7915867/working /scratch/stefan/7915867 Finished preparing REAL250005014398 Recording results /scratch/stefan/7915867/working /scratch/stefan/7915867 Appending to /scratch/stefan/7915867/finished/xaaaaaa.* 0: /scratch/stefan/7915867/working/building/REAL250005014398/0.* Removing working files in /scratch/stefan/7915867/working/building/REAL250005014398 Building REAL250005014399 mkdir: created directory `/scratch/stefan/7915867/working/building/REAL250005014399' /scratch/stefan/7915867/working/building/REAL250005014399 /scratch/stefan/7915867/working /scratch/stefan/7915867 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005014399 mkdir: created directory `0' /scratch/stefan/7915867/working/building/REAL250005014399/0 /scratch/stefan/7915867/working/building/REAL250005014399 /scratch/stefan/7915867/working /scratch/stefan/7915867 Protomer 0 (index: 17) Found valid previously generated 3D confromation in /scratch/stefan/7915867/working/3D/17 `/scratch/stefan/7915867/working/3D/17' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNS(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-]) `REAL250005014399.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005014399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7915867/working/building/REAL250005014399/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014399 none CCNS(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 5, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 5, 1, 1] 7 rigid atoms, others: [3, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 4, 5, 15, 16, 17, 18, 19, 20]) total number of confs: 30 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7915867/working/building/REAL250005014399 /scratch/stefan/7915867/working /scratch/stefan/7915867 Finished preparing REAL250005014399 Recording results /scratch/stefan/7915867/working /scratch/stefan/7915867 Appending to /scratch/stefan/7915867/finished/xaaaaaa.* 0: /scratch/stefan/7915867/working/building/REAL250005014399/0.* Removing working files in /scratch/stefan/7915867/working/building/REAL250005014399 Building REAL250005014400 mkdir: created directory `/scratch/stefan/7915867/working/building/REAL250005014400' /scratch/stefan/7915867/working/building/REAL250005014400 /scratch/stefan/7915867/working /scratch/stefan/7915867 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005014400 mkdir: created directory `0' /scratch/stefan/7915867/working/building/REAL250005014400/0 /scratch/stefan/7915867/working/building/REAL250005014400 /scratch/stefan/7915867/working /scratch/stefan/7915867 Protomer 0 (index: 18) Found valid previously generated 3D confromation in /scratch/stefan/7915867/working/3D/18 `/scratch/stefan/7915867/working/3D/18' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CC)S(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-]) `REAL250005014400.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005014400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7915867/working/building/REAL250005014400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014400 none CCN(CC)S(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 14, 11, 11, 1, 1, 1, 16, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 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: [22, 13, 7, 13, 20, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 20, 20, 20, 20, 20, 1, 1] 27 rigid atoms, others: [5, 8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28] set([0, 1, 2, 3, 4, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 136 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7915867/working/building/REAL250005014400 /scratch/stefan/7915867/working /scratch/stefan/7915867 Finished preparing REAL250005014400 Recording results /scratch/stefan/7915867/working /scratch/stefan/7915867 Appending to /scratch/stefan/7915867/finished/xaaaaaa.* 0: /scratch/stefan/7915867/working/building/REAL250005014400/0.* Removing working files in /scratch/stefan/7915867/working/building/REAL250005014400 Building REAL250005014401 mkdir: created directory `/scratch/stefan/7915867/working/building/REAL250005014401' /scratch/stefan/7915867/working/building/REAL250005014401 /scratch/stefan/7915867/working /scratch/stefan/7915867 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005014401 mkdir: created directory `0' /scratch/stefan/7915867/working/building/REAL250005014401/0 /scratch/stefan/7915867/working/building/REAL250005014401 /scratch/stefan/7915867/working /scratch/stefan/7915867 Protomer 0 (index: 19) Found valid previously generated 3D confromation in /scratch/stefan/7915867/working/3D/19 `/scratch/stefan/7915867/working/3D/19' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C1CC1)S(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-]) `REAL250005014401.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005014401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7915867/working/building/REAL250005014401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014401 none CN(C1CC1)S(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 14, 11, 11, 1, 1, 1, 16, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 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: [6, 1, 1, 1, 1, 6, 15, 15, 15, 23, 23, 23, 22, 23, 23, 23, 23, 6, 6, 6, 1, 1, 1, 1, 1, 23, 23] 23 rigid atoms, others: [1, 2, 3, 4, 20, 21, 22, 23, 24] set([0, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26]) total number of confs: 72 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014401 none CN(C1CC1)S(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 14, 11, 11, 1, 1, 1, 16, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 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: [13, 7, 13, 23, 23, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 23, 23, 23, 23, 23, 1, 1] 23 rigid atoms, others: [5, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26] set([0, 1, 2, 3, 4, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 86 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7915867/working/building/REAL250005014401 /scratch/stefan/7915867/working /scratch/stefan/7915867 Finished preparing REAL250005014401 Recording results /scratch/stefan/7915867/working /scratch/stefan/7915867 Appending to /scratch/stefan/7915867/finished/xaaaaaa.* 0: /scratch/stefan/7915867/working/building/REAL250005014401/0.* Removing working files in /scratch/stefan/7915867/working/building/REAL250005014401 Building REAL250005014402 mkdir: created directory `/scratch/stefan/7915867/working/building/REAL250005014402' /scratch/stefan/7915867/working/building/REAL250005014402 /scratch/stefan/7915867/working /scratch/stefan/7915867 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005014402 mkdir: created directory `0' /scratch/stefan/7915867/working/building/REAL250005014402/0 /scratch/stefan/7915867/working/building/REAL250005014402 /scratch/stefan/7915867/working /scratch/stefan/7915867 Protomer 0 (index: 20) Found valid previously generated 3D confromation in /scratch/stefan/7915867/working/3D/20 `/scratch/stefan/7915867/working/3D/20' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C)S(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-]) `REAL250005014402.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005014402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7915867/working/building/REAL250005014402/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014402 none CCCN(C)S(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 14, 11, 11, 1, 1, 1, 16, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 17, 7, 17, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 39, 39, 17, 17, 17, 1, 1] 41 rigid atoms, others: [5, 8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28] set([0, 1, 2, 3, 4, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7915867/working/building/REAL250005014402 /scratch/stefan/7915867/working /scratch/stefan/7915867 Finished preparing REAL250005014402 Recording results /scratch/stefan/7915867/working /scratch/stefan/7915867 Appending to /scratch/stefan/7915867/finished/xaaaaaa.* 0: /scratch/stefan/7915867/working/building/REAL250005014402/0.* Removing working files in /scratch/stefan/7915867/working/building/REAL250005014402 Building REAL250005014403 mkdir: created directory `/scratch/stefan/7915867/working/building/REAL250005014403' /scratch/stefan/7915867/working/building/REAL250005014403 /scratch/stefan/7915867/working /scratch/stefan/7915867 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005014403 mkdir: created directory `0' /scratch/stefan/7915867/working/building/REAL250005014403/0 /scratch/stefan/7915867/working/building/REAL250005014403 /scratch/stefan/7915867/working /scratch/stefan/7915867 Protomer 0 (index: 21) Found valid previously generated 3D confromation in /scratch/stefan/7915867/working/3D/21 `/scratch/stefan/7915867/working/3D/21' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCCNS(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-]) `REAL250005014403.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005014403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7915867/working/building/REAL250005014403/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014403 none C#CCCNS(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-] NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 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, 31, 13, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 31, 31, 13, 1, 1] 45 rigid atoms, others: [5, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 6, 7, 17, 18, 19, 20, 21, 22]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7915867/working/building/REAL250005014403 /scratch/stefan/7915867/working /scratch/stefan/7915867 Finished preparing REAL250005014403 Recording results /scratch/stefan/7915867/working /scratch/stefan/7915867 Appending to /scratch/stefan/7915867/finished/xaaaaaa.* 0: /scratch/stefan/7915867/working/building/REAL250005014403/0.* Removing working files in /scratch/stefan/7915867/working/building/REAL250005014403 Building REAL250005014404 mkdir: created directory `/scratch/stefan/7915867/working/building/REAL250005014404' /scratch/stefan/7915867/working/building/REAL250005014404 /scratch/stefan/7915867/working /scratch/stefan/7915867 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005014404 mkdir: created directory `0' /scratch/stefan/7915867/working/building/REAL250005014404/0 /scratch/stefan/7915867/working/building/REAL250005014404 /scratch/stefan/7915867/working /scratch/stefan/7915867 Protomer 0 (index: 22) Found valid previously generated 3D confromation in /scratch/stefan/7915867/working/3D/22 `/scratch/stefan/7915867/working/3D/22' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(NS(=O)(=O)C2=CC(Cl)=CC(Cl)=C2[O-])CC1) `REAL250005014404.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005014404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7915867/working/building/REAL250005014404/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014404 none CC1(NS(=O)(=O)C2=CC(Cl)=CC(Cl)=C2[O-])CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 16, 1, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 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, 5, 9, 9, 9, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 2, 2, 2, 5, 13, 13, 1, 1, 1, 1] 13 rigid atoms, others: [0, 1, 2, 15, 16, 23, 24, 25, 26] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 17, 18, 19, 20, 21, 22]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014404 none CC1(NS(=O)(=O)C2=CC(Cl)=CC(Cl)=C2[O-])CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 16, 1, 12, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [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] 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, 7, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 7, 1, 1, 13, 13, 13, 13] 13 rigid atoms, others: [3, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22] set([0, 1, 2, 4, 5, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26]) total number of confs: 46 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7915867/working/building/REAL250005014404 /scratch/stefan/7915867/working /scratch/stefan/7915867 Finished preparing REAL250005014404 Recording results /scratch/stefan/7915867/working /scratch/stefan/7915867 Appending to /scratch/stefan/7915867/finished/xaaaaaa.* 0: /scratch/stefan/7915867/working/building/REAL250005014404/0.* Removing working files in /scratch/stefan/7915867/working/building/REAL250005014404 Building REAL250005014405 mkdir: created directory `/scratch/stefan/7915867/working/building/REAL250005014405' /scratch/stefan/7915867/working/building/REAL250005014405 /scratch/stefan/7915867/working /scratch/stefan/7915867 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005014405 mkdir: created directory `0' /scratch/stefan/7915867/working/building/REAL250005014405/0 /scratch/stefan/7915867/working/building/REAL250005014405 /scratch/stefan/7915867/working /scratch/stefan/7915867 Protomer 0 (index: 23) Found valid previously generated 3D confromation in /scratch/stefan/7915867/working/3D/23 `/scratch/stefan/7915867/working/3D/23' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCN(C)S(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-]) `REAL250005014405.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005014405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7915867/working/building/REAL250005014405/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014405 none CCCN(C)S(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 5, 14, 11, 11, 1, 1, 1, 16, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 17, 7, 17, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 39, 39, 17, 17, 17, 1, 1] 41 rigid atoms, others: [5, 8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28] set([0, 1, 2, 3, 4, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7915867/working/building/REAL250005014405 /scratch/stefan/7915867/working /scratch/stefan/7915867 Finished preparing REAL250005014405 Recording results /scratch/stefan/7915867/working /scratch/stefan/7915867 Appending to /scratch/stefan/7915867/finished/xaaaaaa.* 0: /scratch/stefan/7915867/working/building/REAL250005014405/0.* Removing working files in /scratch/stefan/7915867/working/building/REAL250005014405 Building REAL250005014406 mkdir: created directory `/scratch/stefan/7915867/working/building/REAL250005014406' /scratch/stefan/7915867/working/building/REAL250005014406 /scratch/stefan/7915867/working /scratch/stefan/7915867 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005014406 mkdir: created directory `0' /scratch/stefan/7915867/working/building/REAL250005014406/0 /scratch/stefan/7915867/working/building/REAL250005014406 /scratch/stefan/7915867/working /scratch/stefan/7915867 Protomer 0 (index: 24) Found valid previously generated 3D confromation in /scratch/stefan/7915867/working/3D/24 `/scratch/stefan/7915867/working/3D/24' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=S(=O)(NCCO)C1=CC(Cl)=CC(Cl)=C1[O-]) `REAL250005014406.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005014406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7915867/working/building/REAL250005014406/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014406 none O=S(=O)(NCCO)C1=CC(Cl)=CC(Cl)=C1[O-] NO_LONG_NAME dock atom types: ['O.2', 'S.o2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 14, 11, 8, 5, 5, 12, 1, 1, 1, 16, 1, 1, 16, 1, 12, 6, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 7, 6, 4, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 1 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: [7, 1, 7, 7, 13, 25, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 25, 25, 31, 31, 93, 1, 1] 93 rigid atoms, others: [1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23] set([0, 2, 3, 4, 5, 6, 16, 17, 18, 19, 20, 21]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7915867/working/building/REAL250005014406 /scratch/stefan/7915867/working /scratch/stefan/7915867 Finished preparing REAL250005014406 Recording results /scratch/stefan/7915867/working /scratch/stefan/7915867 Appending to /scratch/stefan/7915867/finished/xaaaaaa.* 0: /scratch/stefan/7915867/working/building/REAL250005014406/0.* Removing working files in /scratch/stefan/7915867/working/building/REAL250005014406 Building REAL250005014407 mkdir: created directory `/scratch/stefan/7915867/working/building/REAL250005014407' /scratch/stefan/7915867/working/building/REAL250005014407 /scratch/stefan/7915867/working /scratch/stefan/7915867 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005014407 mkdir: created directory `0' /scratch/stefan/7915867/working/building/REAL250005014407/0 /scratch/stefan/7915867/working/building/REAL250005014407 /scratch/stefan/7915867/working /scratch/stefan/7915867 Protomer 0 (index: 25) Found valid previously generated 3D confromation in /scratch/stefan/7915867/working/3D/25 `/scratch/stefan/7915867/working/3D/25' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C)S(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-]) `REAL250005014407.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005014407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7915867/working/building/REAL250005014407/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014407 none CCN(C)S(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 14, 11, 11, 1, 1, 1, 16, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 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, 11, 7, 11, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 11, 11, 11, 1, 1] 19 rigid atoms, others: [4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25] set([0, 1, 2, 3, 5, 6, 16, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7915867/working/building/REAL250005014407 /scratch/stefan/7915867/working /scratch/stefan/7915867 Finished preparing REAL250005014407 Recording results /scratch/stefan/7915867/working /scratch/stefan/7915867 Appending to /scratch/stefan/7915867/finished/xaaaaaa.* 0: /scratch/stefan/7915867/working/building/REAL250005014407/0.* Removing working files in /scratch/stefan/7915867/working/building/REAL250005014407 Building REAL250005014408 mkdir: created directory `/scratch/stefan/7915867/working/building/REAL250005014408' /scratch/stefan/7915867/working/building/REAL250005014408 /scratch/stefan/7915867/working /scratch/stefan/7915867 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005014408 mkdir: created directory `0' /scratch/stefan/7915867/working/building/REAL250005014408/0 /scratch/stefan/7915867/working/building/REAL250005014408 /scratch/stefan/7915867/working /scratch/stefan/7915867 Protomer 0 (index: 26) Found valid previously generated 3D confromation in /scratch/stefan/7915867/working/3D/26 `/scratch/stefan/7915867/working/3D/26' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CC(C)NS(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-]) `REAL250005014408.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005014408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7915867/working/building/REAL250005014408/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014408 none C=CC(C)NS(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-] NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 10, 18, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18, 10, 1, 1] 18 rigid atoms, others: [5, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26] set([0, 1, 2, 3, 4, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 71 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7915867/working/building/REAL250005014408 /scratch/stefan/7915867/working /scratch/stefan/7915867 Finished preparing REAL250005014408 Recording results /scratch/stefan/7915867/working /scratch/stefan/7915867 Appending to /scratch/stefan/7915867/finished/xaaaaaa.* 0: /scratch/stefan/7915867/working/building/REAL250005014408/0.* Removing working files in /scratch/stefan/7915867/working/building/REAL250005014408 Building REAL250005014409 mkdir: created directory `/scratch/stefan/7915867/working/building/REAL250005014409' /scratch/stefan/7915867/working/building/REAL250005014409 /scratch/stefan/7915867/working /scratch/stefan/7915867 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005014409 mkdir: created directory `0' /scratch/stefan/7915867/working/building/REAL250005014409/0 /scratch/stefan/7915867/working/building/REAL250005014409 /scratch/stefan/7915867/working /scratch/stefan/7915867 Protomer 0 (index: 27) Found valid previously generated 3D confromation in /scratch/stefan/7915867/working/3D/27 `/scratch/stefan/7915867/working/3D/27' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CN(S(=O)(=O)C2=CC(Cl)=CC(Cl)=C2[O-])C1) `REAL250005014409.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005014409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7915867/working/building/REAL250005014409/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014409 none CC1CN(S(=O)(=O)C2=CC(Cl)=CC(Cl)=C2[O-])C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 16, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 1, 2, 2, 2, 1, 1, 1, 5, 5, 1, 1] 5 rigid atoms, others: [0, 1, 2, 3, 4, 16, 20, 21, 22, 25, 26] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 23, 24]) total number of confs: 21 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014409 none CC1CN(S(=O)(=O)C2=CC(Cl)=CC(Cl)=C2[O-])C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 16, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 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 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, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 1, 1, 5, 5] 5 rigid atoms, others: [4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24] set([0, 1, 2, 3, 5, 6, 16, 17, 18, 19, 20, 21, 22, 25, 26]) total number of confs: 16 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7915867/working/building/REAL250005014409 /scratch/stefan/7915867/working /scratch/stefan/7915867 Finished preparing REAL250005014409 Recording results /scratch/stefan/7915867/working /scratch/stefan/7915867 Appending to /scratch/stefan/7915867/finished/xaaaaaa.* 0: /scratch/stefan/7915867/working/building/REAL250005014409/0.* Removing working files in /scratch/stefan/7915867/working/building/REAL250005014409 Building REAL250005014410 mkdir: created directory `/scratch/stefan/7915867/working/building/REAL250005014410' /scratch/stefan/7915867/working/building/REAL250005014410 /scratch/stefan/7915867/working /scratch/stefan/7915867 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005014410 mkdir: created directory `0' /scratch/stefan/7915867/working/building/REAL250005014410/0 /scratch/stefan/7915867/working/building/REAL250005014410 /scratch/stefan/7915867/working /scratch/stefan/7915867 Protomer 0 (index: 28) Found valid previously generated 3D confromation in /scratch/stefan/7915867/working/3D/28 `/scratch/stefan/7915867/working/3D/28' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=S(=O)(C1=CC(Cl)=CC(Cl)=C1[O-])N1CCCO1) `REAL250005014410.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005014410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7915867/working/building/REAL250005014410/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014410 none O=S(=O)(C1=CC(Cl)=CC(Cl)=C1[O-])N1CCCO1 NO_LONG_NAME dock atom types: ['O.2', 'S.o2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 14, 11, 1, 1, 1, 16, 1, 1, 16, 1, 12, 8, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 1, 1, 7, 7, 7, 7, 7, 7] 7 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18] set([0, 2, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24]) total number of confs: 20 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014410 none O=S(=O)(C1=CC(Cl)=CC(Cl)=C1[O-])N1CCCO1 NO_LONG_NAME dock atom types: ['O.2', 'S.o2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 14, 11, 1, 1, 1, 16, 1, 1, 16, 1, 12, 8, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 7, 7, 1, 1, 1, 1, 1, 1] 7 rigid atoms, others: [1, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18]) total number of confs: 20 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7915867/working/building/REAL250005014410 /scratch/stefan/7915867/working /scratch/stefan/7915867 Finished preparing REAL250005014410 Recording results /scratch/stefan/7915867/working /scratch/stefan/7915867 Appending to /scratch/stefan/7915867/finished/xaaaaaa.* 0: /scratch/stefan/7915867/working/building/REAL250005014410/0.* Removing working files in /scratch/stefan/7915867/working/building/REAL250005014410 Building REAL250005014411 mkdir: created directory `/scratch/stefan/7915867/working/building/REAL250005014411' /scratch/stefan/7915867/working/building/REAL250005014411 /scratch/stefan/7915867/working /scratch/stefan/7915867 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005014411 mkdir: created directory `0' /scratch/stefan/7915867/working/building/REAL250005014411/0 /scratch/stefan/7915867/working/building/REAL250005014411 /scratch/stefan/7915867/working /scratch/stefan/7915867 Protomer 0 (index: 29) Found valid previously generated 3D confromation in /scratch/stefan/7915867/working/3D/29 `/scratch/stefan/7915867/working/3D/29' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCN(C)S(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-]) `REAL250005014411.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005014411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7915867/working/building/REAL250005014411/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014411 none C=CCN(C)S(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-] NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 5, 14, 11, 11, 1, 1, 1, 16, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 43, 19, 7, 19, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 43, 43, 19, 19, 19, 1, 1] 45 rigid atoms, others: [5, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26] set([0, 1, 2, 3, 4, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7915867/working/building/REAL250005014411 /scratch/stefan/7915867/working /scratch/stefan/7915867 Finished preparing REAL250005014411 Recording results /scratch/stefan/7915867/working /scratch/stefan/7915867 Appending to /scratch/stefan/7915867/finished/xaaaaaa.* 0: /scratch/stefan/7915867/working/building/REAL250005014411/0.* Removing working files in /scratch/stefan/7915867/working/building/REAL250005014411 Building REAL250005014412 mkdir: created directory `/scratch/stefan/7915867/working/building/REAL250005014412' /scratch/stefan/7915867/working/building/REAL250005014412 /scratch/stefan/7915867/working /scratch/stefan/7915867 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005014412 mkdir: created directory `0' /scratch/stefan/7915867/working/building/REAL250005014412/0 /scratch/stefan/7915867/working/building/REAL250005014412 /scratch/stefan/7915867/working /scratch/stefan/7915867 Protomer 0 (index: 30) Found valid previously generated 3D confromation in /scratch/stefan/7915867/working/3D/30 `/scratch/stefan/7915867/working/3D/30' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C(C)CNS(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-]) `REAL250005014412.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005014412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7915867/working/building/REAL250005014412/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014412 none C=C(C)CNS(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-] NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 15, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 33, 15, 1, 1] 33 rigid atoms, others: [5, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26] set([0, 1, 2, 3, 4, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7915867/working/building/REAL250005014412 /scratch/stefan/7915867/working /scratch/stefan/7915867 Finished preparing REAL250005014412 Recording results /scratch/stefan/7915867/working /scratch/stefan/7915867 Appending to /scratch/stefan/7915867/finished/xaaaaaa.* 0: /scratch/stefan/7915867/working/building/REAL250005014412/0.* Removing working files in /scratch/stefan/7915867/working/building/REAL250005014412 Building REAL250005014413 mkdir: created directory `/scratch/stefan/7915867/working/building/REAL250005014413' /scratch/stefan/7915867/working/building/REAL250005014413 /scratch/stefan/7915867/working /scratch/stefan/7915867 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005014413 mkdir: created directory `0' /scratch/stefan/7915867/working/building/REAL250005014413/0 /scratch/stefan/7915867/working/building/REAL250005014413 /scratch/stefan/7915867/working /scratch/stefan/7915867 Protomer 0 (index: 31) Found valid previously generated 3D confromation in /scratch/stefan/7915867/working/3D/31 `/scratch/stefan/7915867/working/3D/31' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: N#CCCNS(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-]) `REAL250005014413.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005014413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7915867/working/building/REAL250005014413/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014413 none N#CCCNS(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-] NO_LONG_NAME dock atom types: ['N.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [8, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 16, 1, 12, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 27, 9, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 27, 27, 9, 1, 1] 37 rigid atoms, others: [5, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23] set([0, 1, 2, 3, 4, 6, 7, 17, 18, 19, 20, 21]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7915867/working/building/REAL250005014413 /scratch/stefan/7915867/working /scratch/stefan/7915867 Finished preparing REAL250005014413 Recording results /scratch/stefan/7915867/working /scratch/stefan/7915867 Appending to /scratch/stefan/7915867/finished/xaaaaaa.* 0: /scratch/stefan/7915867/working/building/REAL250005014413/0.* Removing working files in /scratch/stefan/7915867/working/building/REAL250005014413 Building REAL250005014414 mkdir: created directory `/scratch/stefan/7915867/working/building/REAL250005014414' /scratch/stefan/7915867/working/building/REAL250005014414 /scratch/stefan/7915867/working /scratch/stefan/7915867 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005014414 mkdir: created directory `0' /scratch/stefan/7915867/working/building/REAL250005014414/0 /scratch/stefan/7915867/working/building/REAL250005014414 /scratch/stefan/7915867/working /scratch/stefan/7915867 Protomer 0 (index: 32) Found valid previously generated 3D confromation in /scratch/stefan/7915867/working/3D/32 `/scratch/stefan/7915867/working/3D/32' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=S(=O)(NCCF)C1=CC(Cl)=CC(Cl)=C1[O-]) `REAL250005014414.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005014414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7915867/working/building/REAL250005014414/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014414 none O=S(=O)(NCCF)C1=CC(Cl)=CC(Cl)=C1[O-] NO_LONG_NAME dock atom types: ['O.2', 'S.o2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'F', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 14, 11, 8, 5, 5, 15, 1, 1, 1, 16, 1, 1, 16, 1, 12, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 1, 5, 5, 9, 29, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 29, 29, 31, 31, 1, 1] 31 rigid atoms, others: [1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22] set([0, 2, 3, 4, 5, 6, 16, 17, 18, 19, 20]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7915867/working/building/REAL250005014414 /scratch/stefan/7915867/working /scratch/stefan/7915867 Finished preparing REAL250005014414 Recording results /scratch/stefan/7915867/working /scratch/stefan/7915867 Appending to /scratch/stefan/7915867/finished/xaaaaaa.* 0: /scratch/stefan/7915867/working/building/REAL250005014414/0.* Removing working files in /scratch/stefan/7915867/working/building/REAL250005014414 Building REAL250005014415 mkdir: created directory `/scratch/stefan/7915867/working/building/REAL250005014415' /scratch/stefan/7915867/working/building/REAL250005014415 /scratch/stefan/7915867/working /scratch/stefan/7915867 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005014415 mkdir: created directory `0' /scratch/stefan/7915867/working/building/REAL250005014415/0 /scratch/stefan/7915867/working/building/REAL250005014415 /scratch/stefan/7915867/working /scratch/stefan/7915867 Protomer 0 (index: 33) Found valid previously generated 3D confromation in /scratch/stefan/7915867/working/3D/33 `/scratch/stefan/7915867/working/3D/33' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CC(C)NS(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-]) `REAL250005014415.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005014415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7915867/working/building/REAL250005014415/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014415 none C#CC(C)NS(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-] NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 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, 8, 11, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 8, 1, 1] 11 rigid atoms, others: [5, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 6, 7, 17, 18, 19, 20, 21, 22]) total number of confs: 44 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7915867/working/building/REAL250005014415 /scratch/stefan/7915867/working /scratch/stefan/7915867 Finished preparing REAL250005014415 Recording results /scratch/stefan/7915867/working /scratch/stefan/7915867 Appending to /scratch/stefan/7915867/finished/xaaaaaa.* 0: /scratch/stefan/7915867/working/building/REAL250005014415/0.* Removing working files in /scratch/stefan/7915867/working/building/REAL250005014415 Building REAL250005014416 mkdir: created directory `/scratch/stefan/7915867/working/building/REAL250005014416' /scratch/stefan/7915867/working/building/REAL250005014416 /scratch/stefan/7915867/working /scratch/stefan/7915867 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005014416 mkdir: created directory `0' /scratch/stefan/7915867/working/building/REAL250005014416/0 /scratch/stefan/7915867/working/building/REAL250005014416 /scratch/stefan/7915867/working /scratch/stefan/7915867 Protomer 0 (index: 34) Found valid previously generated 3D confromation in /scratch/stefan/7915867/working/3D/34 `/scratch/stefan/7915867/working/3D/34' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C#CCN(C)S(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-]) `REAL250005014416.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005014416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7915867/working/building/REAL250005014416/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014416 none C#CCN(C)S(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-] NO_LONG_NAME dock atom types: ['C.1', 'C.1', 'C.3', 'N.pl3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 8, 5, 14, 11, 11, 1, 1, 1, 16, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 15, 7, 15, 1, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 15, 15, 15, 1, 1] 30 rigid atoms, others: [5, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 6, 7, 17, 18, 19, 20, 21, 22]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7915867/working/building/REAL250005014416 /scratch/stefan/7915867/working /scratch/stefan/7915867 Finished preparing REAL250005014416 Recording results /scratch/stefan/7915867/working /scratch/stefan/7915867 Appending to /scratch/stefan/7915867/finished/xaaaaaa.* 0: /scratch/stefan/7915867/working/building/REAL250005014416/0.* Removing working files in /scratch/stefan/7915867/working/building/REAL250005014416 Building REAL250005014417 mkdir: created directory `/scratch/stefan/7915867/working/building/REAL250005014417' /scratch/stefan/7915867/working/building/REAL250005014417 /scratch/stefan/7915867/working /scratch/stefan/7915867 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005014417 mkdir: created directory `0' /scratch/stefan/7915867/working/building/REAL250005014417/0 /scratch/stefan/7915867/working/building/REAL250005014417 /scratch/stefan/7915867/working /scratch/stefan/7915867 Protomer 0 (index: 35) Found valid previously generated 3D confromation in /scratch/stefan/7915867/working/3D/35 `/scratch/stefan/7915867/working/3D/35' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=S(=O)(NC1CCC1)C1=CC(Cl)=CC(Cl)=C1[O-]) `REAL250005014417.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005014417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7915867/working/building/REAL250005014417/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014417 none O=S(=O)(NC1CCC1)C1=CC(Cl)=CC(Cl)=C1[O-] NO_LONG_NAME dock atom types: ['O.2', 'S.o2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 14, 11, 8, 5, 5, 5, 5, 1, 1, 1, 16, 1, 1, 16, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 13, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 6, 1, 1, 1, 1, 1, 1, 1, 13, 13] 13 rigid atoms, others: [3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014417 none O=S(=O)(NC1CCC1)C1=CC(Cl)=CC(Cl)=C1[O-] NO_LONG_NAME dock atom types: ['O.2', 'S.o2', 'O.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 14, 11, 8, 5, 5, 5, 5, 1, 1, 1, 16, 1, 1, 16, 1, 12, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 5, 7, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 13, 13, 13, 13, 1, 1] 13 rigid atoms, others: [1, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26] set([0, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 48 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7915867/working/building/REAL250005014417 /scratch/stefan/7915867/working /scratch/stefan/7915867 Finished preparing REAL250005014417 Recording results /scratch/stefan/7915867/working /scratch/stefan/7915867 Appending to /scratch/stefan/7915867/finished/xaaaaaa.* 0: /scratch/stefan/7915867/working/building/REAL250005014417/0.* Removing working files in /scratch/stefan/7915867/working/building/REAL250005014417 Building REAL250005014418 mkdir: created directory `/scratch/stefan/7915867/working/building/REAL250005014418' /scratch/stefan/7915867/working/building/REAL250005014418 /scratch/stefan/7915867/working /scratch/stefan/7915867 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005014418 mkdir: created directory `0' /scratch/stefan/7915867/working/building/REAL250005014418/0 /scratch/stefan/7915867/working/building/REAL250005014418 /scratch/stefan/7915867/working /scratch/stefan/7915867 Protomer 0 (index: 36) Found valid previously generated 3D confromation in /scratch/stefan/7915867/working/3D/36 `/scratch/stefan/7915867/working/3D/36' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=S(=O)(C1=CC(Cl)=CC(Cl)=C1[O-])N1CC=CC1) `REAL250005014418.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005014418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7915867/working/building/REAL250005014418/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014418 none O=S(=O)(C1=CC(Cl)=CC(Cl)=C1[O-])N1CC=CC1 NO_LONG_NAME dock atom types: ['O.2', 'S.o2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 14, 11, 1, 1, 1, 16, 1, 1, 16, 1, 12, 8, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 6, 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 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 5, 5, 5, 5, 5, 5] 5 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18] set([0, 2, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24]) total number of confs: 16 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014418 none O=S(=O)(C1=CC(Cl)=CC(Cl)=C1[O-])N1CC=CC1 NO_LONG_NAME dock atom types: ['O.2', 'S.o2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 14, 11, 1, 1, 1, 16, 1, 1, 16, 1, 12, 8, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 6, 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 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 5, 5, 1, 1, 1, 1, 1, 1] 5 rigid atoms, others: [1, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 17, 18]) total number of confs: 12 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7915867/working/building/REAL250005014418 /scratch/stefan/7915867/working /scratch/stefan/7915867 Finished preparing REAL250005014418 Recording results /scratch/stefan/7915867/working /scratch/stefan/7915867 Appending to /scratch/stefan/7915867/finished/xaaaaaa.* 0: /scratch/stefan/7915867/working/building/REAL250005014418/0.* Removing working files in /scratch/stefan/7915867/working/building/REAL250005014418 Building REAL250005014419 mkdir: created directory `/scratch/stefan/7915867/working/building/REAL250005014419' /scratch/stefan/7915867/working/building/REAL250005014419 /scratch/stefan/7915867/working /scratch/stefan/7915867 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005014419 mkdir: created directory `0' /scratch/stefan/7915867/working/building/REAL250005014419/0 /scratch/stefan/7915867/working/building/REAL250005014419 /scratch/stefan/7915867/working /scratch/stefan/7915867 Protomer 0 (index: 37) Found valid previously generated 3D confromation in /scratch/stefan/7915867/working/3D/37 `/scratch/stefan/7915867/working/3D/37' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C=CCNS(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-]) `REAL250005014419.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005014419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7915867/working/building/REAL250005014419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014419 none C=C=CCNS(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-] NO_LONG_NAME dock atom types: ['C.2', 'C.1', 'C.2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 1, 5, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 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, 49, 15, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 75, 75, 75, 49, 49, 15, 1, 1] 75 rigid atoms, others: [5, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24] set([0, 1, 2, 3, 4, 6, 7, 17, 18, 19, 20, 21, 22]) total number of confs: 260 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7915867/working/building/REAL250005014419 /scratch/stefan/7915867/working /scratch/stefan/7915867 Finished preparing REAL250005014419 Recording results /scratch/stefan/7915867/working /scratch/stefan/7915867 Appending to /scratch/stefan/7915867/finished/xaaaaaa.* 0: /scratch/stefan/7915867/working/building/REAL250005014419/0.* Removing working files in /scratch/stefan/7915867/working/building/REAL250005014419 Building REAL250005014420 mkdir: created directory `/scratch/stefan/7915867/working/building/REAL250005014420' /scratch/stefan/7915867/working/building/REAL250005014420 /scratch/stefan/7915867/working /scratch/stefan/7915867 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005014420 mkdir: created directory `0' /scratch/stefan/7915867/working/building/REAL250005014420/0 /scratch/stefan/7915867/working/building/REAL250005014420 /scratch/stefan/7915867/working /scratch/stefan/7915867 Protomer 0 (index: 38) Found valid previously generated 3D confromation in /scratch/stefan/7915867/working/3D/38 `/scratch/stefan/7915867/working/3D/38' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=CCCNS(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-]) `REAL250005014420.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005014420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7915867/working/building/REAL250005014420/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014420 none C=CCCNS(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-] NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 60, 14, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 80, 80, 80, 80, 80, 60, 60, 14, 1, 1] 80 rigid atoms, others: [5, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26] set([0, 1, 2, 3, 4, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 330 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7915867/working/building/REAL250005014420 /scratch/stefan/7915867/working /scratch/stefan/7915867 Finished preparing REAL250005014420 Recording results /scratch/stefan/7915867/working /scratch/stefan/7915867 Appending to /scratch/stefan/7915867/finished/xaaaaaa.* 0: /scratch/stefan/7915867/working/building/REAL250005014420/0.* Removing working files in /scratch/stefan/7915867/working/building/REAL250005014420 Building REAL250005014421 mkdir: created directory `/scratch/stefan/7915867/working/building/REAL250005014421' /scratch/stefan/7915867/working/building/REAL250005014421 /scratch/stefan/7915867/working /scratch/stefan/7915867 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005014421 mkdir: created directory `0' /scratch/stefan/7915867/working/building/REAL250005014421/0 /scratch/stefan/7915867/working/building/REAL250005014421 /scratch/stefan/7915867/working /scratch/stefan/7915867 Protomer 0 (index: 39) Found valid previously generated 3D confromation in /scratch/stefan/7915867/working/3D/39 `/scratch/stefan/7915867/working/3D/39' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H]1NS(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-]) `REAL250005014421.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005014421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7915867/working/building/REAL250005014421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014421 none C[C@@H]1C[C@H]1NS(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 10, 10, 10, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 6, 11, 11] 11 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014421 none C[C@@H]1C[C@H]1NS(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 11, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 9, 1, 1] 11 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 19, 20, 21, 22, 23, 24]) total number of confs: 36 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7915867/working/building/REAL250005014421 /scratch/stefan/7915867/working /scratch/stefan/7915867 Finished preparing REAL250005014421 Recording results /scratch/stefan/7915867/working /scratch/stefan/7915867 Appending to /scratch/stefan/7915867/finished/xaaaaaa.* 0: /scratch/stefan/7915867/working/building/REAL250005014421/0.* Removing working files in /scratch/stefan/7915867/working/building/REAL250005014421 Building REAL250005014422 mkdir: created directory `/scratch/stefan/7915867/working/building/REAL250005014422' /scratch/stefan/7915867/working/building/REAL250005014422 /scratch/stefan/7915867/working /scratch/stefan/7915867 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005014422 mkdir: created directory `0' /scratch/stefan/7915867/working/building/REAL250005014422/0 /scratch/stefan/7915867/working/building/REAL250005014422 /scratch/stefan/7915867/working /scratch/stefan/7915867 Protomer 0 (index: 40) Found valid previously generated 3D confromation in /scratch/stefan/7915867/working/3D/40 `/scratch/stefan/7915867/working/3D/40' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H]1NS(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-]) `REAL250005014422.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005014422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7915867/working/building/REAL250005014422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014422 none C[C@@H]1C[C@H]1NS(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 10, 10, 10, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 6, 11, 11] 11 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014422 none C[C@@H]1C[C@H]1NS(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 11, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 9, 1, 1] 11 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 19, 20, 21, 22, 23, 24]) total number of confs: 36 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7915867/working/building/REAL250005014422 /scratch/stefan/7915867/working /scratch/stefan/7915867 Finished preparing REAL250005014422 Recording results /scratch/stefan/7915867/working /scratch/stefan/7915867 Appending to /scratch/stefan/7915867/finished/xaaaaaa.* 0: /scratch/stefan/7915867/working/building/REAL250005014422/0.* Removing working files in /scratch/stefan/7915867/working/building/REAL250005014422 Building REAL250005014423 mkdir: created directory `/scratch/stefan/7915867/working/building/REAL250005014423' /scratch/stefan/7915867/working/building/REAL250005014423 /scratch/stefan/7915867/working /scratch/stefan/7915867 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005014423 mkdir: created directory `0' /scratch/stefan/7915867/working/building/REAL250005014423/0 /scratch/stefan/7915867/working/building/REAL250005014423 /scratch/stefan/7915867/working /scratch/stefan/7915867 Protomer 0 (index: 41) Found valid previously generated 3D confromation in /scratch/stefan/7915867/working/3D/41 `/scratch/stefan/7915867/working/3D/41' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC1NS(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-]) `REAL250005014423.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005014423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7915867/working/building/REAL250005014423/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014423 none CC1CC1NS(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 10, 10, 10, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 1, 1, 6, 11, 11] 11 rigid atoms, others: [0, 1, 2, 3, 4, 20, 21, 22, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014423 none CC1CC1NS(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 9, 1, 1] 11 rigid atoms, others: [5, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26] set([0, 1, 2, 3, 4, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 36 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7915867/working/building/REAL250005014423 /scratch/stefan/7915867/working /scratch/stefan/7915867 Finished preparing REAL250005014423 Recording results /scratch/stefan/7915867/working /scratch/stefan/7915867 Appending to /scratch/stefan/7915867/finished/xaaaaaa.* 0: /scratch/stefan/7915867/working/building/REAL250005014423/0.* Removing working files in /scratch/stefan/7915867/working/building/REAL250005014423 Building REAL250005014424 mkdir: created directory `/scratch/stefan/7915867/working/building/REAL250005014424' /scratch/stefan/7915867/working/building/REAL250005014424 /scratch/stefan/7915867/working /scratch/stefan/7915867 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005014424 mkdir: created directory `0' /scratch/stefan/7915867/working/building/REAL250005014424/0 /scratch/stefan/7915867/working/building/REAL250005014424 /scratch/stefan/7915867/working /scratch/stefan/7915867 Protomer 0 (index: 42) Found valid previously generated 3D confromation in /scratch/stefan/7915867/working/3D/42 `/scratch/stefan/7915867/working/3D/42' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H]1NS(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-]) `REAL250005014424.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005014424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7915867/working/building/REAL250005014424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014424 none C[C@H]1C[C@@H]1NS(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 10, 10, 10, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 6, 11, 11] 11 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26]) total number of confs: 45 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014424 none C[C@H]1C[C@@H]1NS(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 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, 9, 11, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 9, 1, 1] 11 rigid atoms, others: [7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 19, 20, 21, 22, 23, 24]) total number of confs: 36 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7915867/working/building/REAL250005014424 /scratch/stefan/7915867/working /scratch/stefan/7915867 Finished preparing REAL250005014424 Recording results /scratch/stefan/7915867/working /scratch/stefan/7915867 Appending to /scratch/stefan/7915867/finished/xaaaaaa.* 0: /scratch/stefan/7915867/working/building/REAL250005014424/0.* Removing working files in /scratch/stefan/7915867/working/building/REAL250005014424 Building REAL250005014425 mkdir: created directory `/scratch/stefan/7915867/working/building/REAL250005014425' /scratch/stefan/7915867/working/building/REAL250005014425 /scratch/stefan/7915867/working /scratch/stefan/7915867 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005014425 mkdir: created directory `0' /scratch/stefan/7915867/working/building/REAL250005014425/0 /scratch/stefan/7915867/working/building/REAL250005014425 /scratch/stefan/7915867/working /scratch/stefan/7915867 Protomer 0 (index: 43) Found valid previously generated 3D confromation in /scratch/stefan/7915867/working/3D/43 `/scratch/stefan/7915867/working/3D/43' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC=CCNS(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-]) `REAL250005014425.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005014425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7915867/working/building/REAL250005014425/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014425 none CC=CCNS(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 36, 13, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 44, 36, 36, 13, 1, 1] 44 rigid atoms, others: [5, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26] set([0, 1, 2, 3, 4, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7915867/working/building/REAL250005014425 /scratch/stefan/7915867/working /scratch/stefan/7915867 Finished preparing REAL250005014425 Recording results /scratch/stefan/7915867/working /scratch/stefan/7915867 Appending to /scratch/stefan/7915867/finished/xaaaaaa.* 0: /scratch/stefan/7915867/working/building/REAL250005014425/0.* Removing working files in /scratch/stefan/7915867/working/building/REAL250005014425 Building REAL250005014426 mkdir: created directory `/scratch/stefan/7915867/working/building/REAL250005014426' /scratch/stefan/7915867/working/building/REAL250005014426 /scratch/stefan/7915867/working /scratch/stefan/7915867 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005014426 mkdir: created directory `0' /scratch/stefan/7915867/working/building/REAL250005014426/0 /scratch/stefan/7915867/working/building/REAL250005014426 /scratch/stefan/7915867/working /scratch/stefan/7915867 Protomer 0 (index: 44) Found valid previously generated 3D confromation in /scratch/stefan/7915867/working/3D/44 `/scratch/stefan/7915867/working/3D/44' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=S(=O)(C1=CC(Cl)=CC(Cl)=C1[O-])N1CCC1) `REAL250005014426.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005014426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7915867/working/building/REAL250005014426/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014426 none O=S(=O)(C1=CC(Cl)=CC(Cl)=C1[O-])N1CCC1 NO_LONG_NAME dock atom types: ['O.2', 'S.o2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 14, 11, 1, 1, 1, 16, 1, 1, 16, 1, 12, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 6, 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 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 5, 5, 5, 5, 5, 5] 5 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17] set([0, 2, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23]) total number of confs: 16 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014426 none O=S(=O)(C1=CC(Cl)=CC(Cl)=C1[O-])N1CCC1 NO_LONG_NAME dock atom types: ['O.2', 'S.o2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 14, 11, 1, 1, 1, 16, 1, 1, 16, 1, 12, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 6, 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 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 5, 5, 5, 4, 5, 5, 5, 5, 1, 1, 1, 1, 5, 4, 1, 1, 1, 1, 1, 1] 5 rigid atoms, others: [1, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 16, 17]) total number of confs: 16 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7915867/working/building/REAL250005014426 /scratch/stefan/7915867/working /scratch/stefan/7915867 Finished preparing REAL250005014426 Recording results /scratch/stefan/7915867/working /scratch/stefan/7915867 Appending to /scratch/stefan/7915867/finished/xaaaaaa.* 0: /scratch/stefan/7915867/working/building/REAL250005014426/0.* Removing working files in /scratch/stefan/7915867/working/building/REAL250005014426 Building REAL250005014427 mkdir: created directory `/scratch/stefan/7915867/working/building/REAL250005014427' /scratch/stefan/7915867/working/building/REAL250005014427 /scratch/stefan/7915867/working /scratch/stefan/7915867 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005014427 mkdir: created directory `0' /scratch/stefan/7915867/working/building/REAL250005014427/0 /scratch/stefan/7915867/working/building/REAL250005014427 /scratch/stefan/7915867/working /scratch/stefan/7915867 Protomer 0 (index: 45) Found valid previously generated 3D confromation in /scratch/stefan/7915867/working/3D/45 `/scratch/stefan/7915867/working/3D/45' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCNS(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-]) `REAL250005014427.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005014427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7915867/working/building/REAL250005014427/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014427 none CCCNS(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [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] 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, 27, 11, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 27, 27, 11, 1, 1] 37 rigid atoms, others: [4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25] set([0, 1, 2, 3, 5, 6, 16, 17, 18, 19, 20, 21, 22, 23]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7915867/working/building/REAL250005014427 /scratch/stefan/7915867/working /scratch/stefan/7915867 Finished preparing REAL250005014427 Recording results /scratch/stefan/7915867/working /scratch/stefan/7915867 Appending to /scratch/stefan/7915867/finished/xaaaaaa.* 0: /scratch/stefan/7915867/working/building/REAL250005014427/0.* Removing working files in /scratch/stefan/7915867/working/building/REAL250005014427 Building REAL250005014428 mkdir: created directory `/scratch/stefan/7915867/working/building/REAL250005014428' /scratch/stefan/7915867/working/building/REAL250005014428 /scratch/stefan/7915867/working /scratch/stefan/7915867 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005014428 mkdir: created directory `0' /scratch/stefan/7915867/working/building/REAL250005014428/0 /scratch/stefan/7915867/working/building/REAL250005014428 /scratch/stefan/7915867/working /scratch/stefan/7915867 Protomer 0 (index: 46) Found valid previously generated 3D confromation in /scratch/stefan/7915867/working/3D/46 `/scratch/stefan/7915867/working/3D/46' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: [NH3+][C@@H]1C[C@H]1NS(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-]) `REAL250005014428.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005014428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7915867/working/building/REAL250005014428/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014428 none [NH3+][C@@H]1C[C@H]1NS(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-] NO_LONG_NAME dock atom types: ['N.4', 'H', 'H', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [9, 6, 6, 6, 5, 7, 5, 5, 7, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 16, 1, 12, 7, 7, 6, 7, 7] dock color type numbers: [1, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 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, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 2, 3, 3] 3 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 22, 23] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26]) total number of confs: 11 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014428 none [NH3+][C@@H]1C[C@H]1NS(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-] NO_LONG_NAME dock atom types: ['N.4', 'H', 'H', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [9, 6, 6, 6, 5, 7, 5, 5, 7, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 16, 1, 12, 7, 7, 6, 7, 7] dock color type numbers: [1, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1] 3 rigid atoms, others: [10, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 22, 23, 24]) total number of confs: 10 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7915867/working/building/REAL250005014428 /scratch/stefan/7915867/working /scratch/stefan/7915867 Finished preparing REAL250005014428 Recording results /scratch/stefan/7915867/working /scratch/stefan/7915867 Appending to /scratch/stefan/7915867/finished/xaaaaaa.* 0: /scratch/stefan/7915867/working/building/REAL250005014428/0.* Removing working files in /scratch/stefan/7915867/working/building/REAL250005014428 Building REAL250005014429 mkdir: created directory `/scratch/stefan/7915867/working/building/REAL250005014429' /scratch/stefan/7915867/working/building/REAL250005014429 /scratch/stefan/7915867/working /scratch/stefan/7915867 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005014429 mkdir: created directory `0' /scratch/stefan/7915867/working/building/REAL250005014429/0 /scratch/stefan/7915867/working/building/REAL250005014429 /scratch/stefan/7915867/working /scratch/stefan/7915867 Protomer 0 (index: 47) Found valid previously generated 3D confromation in /scratch/stefan/7915867/working/3D/47 `/scratch/stefan/7915867/working/3D/47' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC[NH3+])S(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-]) `REAL250005014429.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005014429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7915867/working/building/REAL250005014429/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014429 none CN(CC[NH3+])S(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'N.4', 'H', 'H', 'H', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 9, 6, 6, 6, 14, 11, 11, 1, 1, 1, 16, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 1, 1] 3 rigid atoms, others: [8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 10 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7915867/working/building/REAL250005014429 /scratch/stefan/7915867/working /scratch/stefan/7915867 Finished preparing REAL250005014429 Recording results /scratch/stefan/7915867/working /scratch/stefan/7915867 Appending to /scratch/stefan/7915867/finished/xaaaaaa.* 0: /scratch/stefan/7915867/working/building/REAL250005014429/0.* Removing working files in /scratch/stefan/7915867/working/building/REAL250005014429 Building REAL250005014430 mkdir: created directory `/scratch/stefan/7915867/working/building/REAL250005014430' /scratch/stefan/7915867/working/building/REAL250005014430 /scratch/stefan/7915867/working /scratch/stefan/7915867 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL250005014430 mkdir: created directory `0' /scratch/stefan/7915867/working/building/REAL250005014430/0 /scratch/stefan/7915867/working/building/REAL250005014430 /scratch/stefan/7915867/working /scratch/stefan/7915867 Protomer 0 (index: 48) Found valid previously generated 3D confromation in /scratch/stefan/7915867/working/3D/48 `/scratch/stefan/7915867/working/3D/48' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]([NH3+])CNS(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-]) `REAL250005014430.mol2' -> `0.mol2' `temp.mol2' -> `REAL250005014430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7915867/working/building/REAL250005014430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL250005014430 none C[C@@H]([NH3+])CNS(=O)(=O)C1=CC(Cl)=CC(Cl)=C1[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.4', 'H', 'H', 'H', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 9, 6, 6, 6, 5, 8, 14, 11, 11, 1, 1, 1, 16, 1, 1, 16, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 1, 7, 7, 7, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 7, 5, 1, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 7, 1, 1] 8 rigid atoms, others: [9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 21, 22, 23, 24, 25, 26]) total number of confs: 30 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7915867/working/building/REAL250005014430 /scratch/stefan/7915867/working /scratch/stefan/7915867 Finished preparing REAL250005014430 Recording results /scratch/stefan/7915867/working /scratch/stefan/7915867 Appending to /scratch/stefan/7915867/finished/xaaaaaa.* 0: /scratch/stefan/7915867/working/building/REAL250005014430/0.* Removing working files in /scratch/stefan/7915867/working/building/REAL250005014430 /scratch/stefan/7915867 Compressing combined databse files /scratch/stefan/7915867/finished/xaaaaaa.db2.gz /scratch/stefan/7915867/finished/xaaaaaa.solv.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/stefan/7915867/finished) ======================================================= Finalizing... removed `/scratch/stefan/7915867/working/3D/49' removed directory: `/scratch/stefan/7915867/working/3D' rmdir: removing directory, `/scratch/stefan/7915867/working/building' rmdir: removing directory, `/scratch/stefan/7915867/working' ls: No match. ls: No match.