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/7774842/working' mkdir: created directory `/scratch/stefan/7774842/working/protonate' Storing results in /scratch/stefan/7774842/finished Working in /scratch/stefan/7774842/working /scratch/stefan/7774842/working /scratch/stefan/7774842 /scratch/stefan/7774842/working/protonate /scratch/stefan/7774842/working /scratch/stefan/7774842 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: 1020 protomers created Coalesing and merging protomers 1009 protomers generated for 1000 compounds Checking for new stereocenters and expanding 1047 protomers after new stereo-center expansion /scratch/stefan/7774842/working /scratch/stefan/7774842 Bulk generating 3D conformations all protomers in /scratch/stefan/7774842/working/3D mkdir: created directory `/scratch/stefan/7774842/working/3D' We are using corina for 3D embeding debuging info:: /scratch/stefan/7774842/working/protonate/xaaaatx-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' 1048 3D conformations generated for 1000 compounds Building REAL300004517001 mkdir: created directory `/scratch/stefan/7774842/working/building' mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517001' /scratch/stefan/7774842/working/building/REAL300004517001 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004517001 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517001/0 /scratch/stefan/7774842/working/building/REAL300004517001 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/1 `/scratch/stefan/7774842/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCC[N@H+](C)C1)C(=O)CN1C=C(C(=O)[O-])C2=CC=CC=C21) `REAL300004517001.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517001 none CN(CC1CCC[N@H+](C)C1)C(=O)CN1C=C(C(=O)[O-])C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 5, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 9, 9, 9, 9, 9, 9, 9, 9, 5, 8, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1] 9 rigid atoms, others: [48, 49, 47, 46, 45, 14, 13, 16, 17, 20, 21, 22, 23, 24, 25, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 36 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517001 none CN(CC1CCC[N@H+](C)C1)C(=O)CN1C=C(C(=O)[O-])C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 5, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 5, 5, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 4, 4, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 7, 7, 9, 9, 9, 9, 9] 9 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 35, 41, 36, 42, 37, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 39 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517001 /scratch/stefan/7774842/working /scratch/stefan/7774842 mkdir: created directory `1' /scratch/stefan/7774842/working/building/REAL300004517001/1 /scratch/stefan/7774842/working/building/REAL300004517001 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 1 (index: 2) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/2 `/scratch/stefan/7774842/working/3D/2' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCC[N@@H+](C)C1)C(=O)CN1C=C(C(=O)[O-])C2=CC=CC=C21) `REAL300004517001.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004517001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517001/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517001 none CN(CC1CCC[N@@H+](C)C1)C(=O)CN1C=C(C(=O)[O-])C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 5, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 9, 9, 9, 9, 9, 9, 9, 9, 5, 8, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 5, 1, 1, 1, 1, 1] 9 rigid atoms, others: [48, 49, 47, 46, 45, 14, 13, 16, 17, 20, 21, 22, 23, 24, 25, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 36 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517001 none CN(CC1CCC[N@@H+](C)C1)C(=O)CN1C=C(C(=O)[O-])C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 5, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 5, 5, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 4, 4, 4, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 7, 7, 9, 9, 9, 9, 9] 9 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 35, 41, 36, 42, 37, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 39 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517001 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517001 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 mkdir: created directory `/scratch/stefan/7774842/finished' Appending to /scratch/stefan/7774842/finished/xaaaatx.* 1: /scratch/stefan/7774842/working/building/REAL300004517001/1.* 0: /scratch/stefan/7774842/working/building/REAL300004517001/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517001 Building REAL300004517002 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517002' /scratch/stefan/7774842/working/building/REAL300004517002 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004517002 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517002/0 /scratch/stefan/7774842/working/building/REAL300004517002 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 3) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/3 `/scratch/stefan/7774842/working/3D/3' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)[O-])C=C1C(=O)N(C)CC1CCC[N@H+](C)C1) `REAL300004517002.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517002 none CC1=CC=C(C(=O)[O-])C=C1C(=O)N(C)CC1CCC[N@H+](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 25, 25, 25, 25, 22, 14, 22, 8, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 14, 14, 14, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1] 25 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43]) total number of confs: 83 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517002 none CC1=CC=C(C(=O)[O-])C=C1C(=O)N(C)CC1CCC[N@H+](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 6, 6, 15, 15, 22, 25, 25, 25, 25, 25, 25, 25, 2, 2, 2, 1, 1, 1, 15, 15, 15, 22, 22, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25] 25 rigid atoms, others: [0, 1, 2, 3, 4, 5, 8, 9, 10, 26, 27, 28] set([6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 103 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517002 /scratch/stefan/7774842/working /scratch/stefan/7774842 mkdir: created directory `1' /scratch/stefan/7774842/working/building/REAL300004517002/1 /scratch/stefan/7774842/working/building/REAL300004517002 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 1 (index: 4) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/4 `/scratch/stefan/7774842/working/3D/4' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)[O-])C=C1C(=O)N(C)CC1CCC[N@@H+](C)C1) `REAL300004517002.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004517002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517002/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517002 none CC1=CC=C(C(=O)[O-])C=C1C(=O)N(C)CC1CCC[N@@H+](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 25, 25, 25, 25, 22, 14, 22, 8, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 14, 14, 14, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1] 25 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43]) total number of confs: 83 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517002 none CC1=CC=C(C(=O)[O-])C=C1C(=O)N(C)CC1CCC[N@@H+](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 15, 15, 22, 25, 25, 25, 25, 25, 25, 25, 2, 2, 2, 1, 1, 1, 15, 15, 15, 22, 22, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25] 25 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 99 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517002 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517002 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 1: /scratch/stefan/7774842/working/building/REAL300004517002/1.* 0: /scratch/stefan/7774842/working/building/REAL300004517002/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517002 Building REAL300004517003 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517003' /scratch/stefan/7774842/working/building/REAL300004517003 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004517003 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517003/0 /scratch/stefan/7774842/working/building/REAL300004517003 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 5) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/5 `/scratch/stefan/7774842/working/3D/5' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=NC=C1C(=O)N(C)CC1CCC[N@H+](C)C1) `REAL300004517003.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517003/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517003 none CC1=C(C(=O)[O-])C=NC=C1C(=O)N(C)CC1CCC[N@H+](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 22, 19, 12, 19, 6, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 12, 12, 12, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1] 22 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 43, 44, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42]) total number of confs: 71 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517003 none CC1=C(C(=O)[O-])C=NC=C1C(=O)N(C)CC1CCC[N@H+](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 5, 5, 13, 13, 20, 22, 22, 22, 22, 22, 22, 22, 2, 2, 2, 1, 1, 13, 13, 13, 20, 20, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 22 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 9, 10, 26, 27] set([4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 86 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517003 /scratch/stefan/7774842/working /scratch/stefan/7774842 mkdir: created directory `1' /scratch/stefan/7774842/working/building/REAL300004517003/1 /scratch/stefan/7774842/working/building/REAL300004517003 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 1 (index: 6) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/6 `/scratch/stefan/7774842/working/3D/6' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=NC=C1C(=O)N(C)CC1CCC[N@@H+](C)C1) `REAL300004517003.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004517003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517003/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517003 none CC1=C(C(=O)[O-])C=NC=C1C(=O)N(C)CC1CCC[N@@H+](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 8, 9, 6, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 8, 8, 8, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1] 9 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 43, 44, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42]) total number of confs: 37 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517003 none CC1=C(C(=O)[O-])C=NC=C1C(=O)N(C)CC1CCC[N@@H+](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 4, 4, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 7, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 9 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 9, 10, 26, 27] set([4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 43 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517003 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517003 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 1: /scratch/stefan/7774842/working/building/REAL300004517003/1.* 0: /scratch/stefan/7774842/working/building/REAL300004517003/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517003 Building REAL300004517004 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517004' /scratch/stefan/7774842/working/building/REAL300004517004 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004517004 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517004/0 /scratch/stefan/7774842/working/building/REAL300004517004 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 7) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/7 `/scratch/stefan/7774842/working/3D/7' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1C(=O)N(C)CC1CCC[N@H+](C)C1) `REAL300004517004.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517004/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517004 none CC1=CC(C(=O)[O-])=CC=C1C(=O)N(C)CC1CCC[N@H+](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 39, 39, 39, 39, 39, 25, 15, 25, 8, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 39, 15, 15, 15, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1] 39 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43]) total number of confs: 111 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517004 none CC1=CC(C(=O)[O-])=CC=C1C(=O)N(C)CC1CCC[N@H+](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 6, 6, 15, 15, 31, 39, 39, 39, 39, 39, 39, 39, 2, 2, 2, 1, 1, 1, 15, 15, 15, 31, 31, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39] 39 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 26, 27, 28] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 159 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517004 /scratch/stefan/7774842/working /scratch/stefan/7774842 mkdir: created directory `1' /scratch/stefan/7774842/working/building/REAL300004517004/1 /scratch/stefan/7774842/working/building/REAL300004517004 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 1 (index: 8) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/8 `/scratch/stefan/7774842/working/3D/8' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1C(=O)N(C)CC1CCC[N@@H+](C)C1) `REAL300004517004.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004517004.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517004/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517004 none CC1=CC(C(=O)[O-])=CC=C1C(=O)N(C)CC1CCC[N@@H+](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 25, 25, 39, 39, 39, 39, 25, 15, 25, 8, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 39, 15, 15, 15, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1] 39 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43]) total number of confs: 209 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517004 none CC1=CC(C(=O)[O-])=CC=C1C(=O)N(C)CC1CCC[N@@H+](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 6, 6, 15, 15, 31, 39, 39, 39, 39, 39, 39, 39, 2, 2, 2, 1, 1, 1, 15, 15, 15, 31, 31, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39] 39 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 26, 27, 28] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 159 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517004 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517004 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 1: /scratch/stefan/7774842/working/building/REAL300004517004/1.* 0: /scratch/stefan/7774842/working/building/REAL300004517004/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517004 Building REAL300004517005 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517005' /scratch/stefan/7774842/working/building/REAL300004517005 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004517005 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517005/0 /scratch/stefan/7774842/working/building/REAL300004517005 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 9) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/9 `/scratch/stefan/7774842/working/3D/9' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCC[N@H+](C)C1)C(=O)C1=CC=C(C(=O)[O-])C=C1Cl) `REAL300004517005.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517005/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517005 none CN(CC1CCC[N@H+](C)C1)C(=O)C1=CC=C(C(=O)[O-])C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [17, 7, 17, 30, 30, 30, 30, 30, 30, 30, 30, 1, 7, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 17, 17, 17, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1] 30 rigid atoms, others: [40, 41, 42, 11, 13, 14, 15, 16, 17, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 114 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517005 none CN(CC1CCC[N@H+](C)C1)C(=O)C1=CC=C(C(=O)[O-])C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 19, 19, 30, 30, 30, 30, 30, 30, 30, 30, 30, 10, 10, 10, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 30, 30, 30] 30 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 39, 34, 38, 28, 29, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 40, 41, 42]) total number of confs: 89 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517005 /scratch/stefan/7774842/working /scratch/stefan/7774842 mkdir: created directory `1' /scratch/stefan/7774842/working/building/REAL300004517005/1 /scratch/stefan/7774842/working/building/REAL300004517005 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 1 (index: 10) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/10 `/scratch/stefan/7774842/working/3D/10' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCC[N@@H+](C)C1)C(=O)C1=CC=C(C(=O)[O-])C=C1Cl) `REAL300004517005.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004517005.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517005/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517005 none CN(CC1CCC[N@@H+](C)C1)C(=O)C1=CC=C(C(=O)[O-])C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [17, 7, 17, 30, 30, 30, 30, 30, 30, 30, 30, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1, 1] 30 rigid atoms, others: [40, 41, 42, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 110 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517005 none CN(CC1CCC[N@@H+](C)C1)C(=O)C1=CC=C(C(=O)[O-])C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 20, 20, 30, 30, 30, 30, 30, 30, 30, 30, 30, 10, 10, 10, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 30, 30, 30] 30 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 39, 34, 38, 28, 29, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 40, 41, 42]) total number of confs: 89 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517005 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517005 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 1: /scratch/stefan/7774842/working/building/REAL300004517005/1.* 0: /scratch/stefan/7774842/working/building/REAL300004517005/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517005 Building REAL300004517006 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517006' /scratch/stefan/7774842/working/building/REAL300004517006 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004517006 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517006/0 /scratch/stefan/7774842/working/building/REAL300004517006 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 11) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/11 `/scratch/stefan/7774842/working/3D/11' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCC[N@H+](C)C1)C(=O)C1CC2(CC(C(=O)[O-])C2)C1) `REAL300004517006.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517006/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517006 none CN(CC1CCC[N@H+](C)C1)C(=O)C1CC2(CC(C(=O)[O-])C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [14, 8, 14, 23, 32, 32, 32, 32, 32, 32, 32, 1, 8, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 14, 14, 14, 23, 23, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 32 rigid atoms, others: [48, 45, 43, 49, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18, 21, 22, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 119 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517006 none CN(CC1CCC[N@H+](C)C1)C(=O)C1CC2(CC(C(=O)[O-])C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [14, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 25, 25, 32, 32, 32, 32, 32, 32, 32, 32, 32, 14, 14, 14, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32] 32 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 39, 34, 38, 28, 29, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 113 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517006 /scratch/stefan/7774842/working /scratch/stefan/7774842 mkdir: created directory `1' /scratch/stefan/7774842/working/building/REAL300004517006/1 /scratch/stefan/7774842/working/building/REAL300004517006 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 1 (index: 12) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/12 `/scratch/stefan/7774842/working/3D/12' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCC[N@@H+](C)C1)C(=O)C1CC2(CC(C(=O)[O-])C2)C1) `REAL300004517006.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004517006.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517006/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517006 none CN(CC1CCC[N@@H+](C)C1)C(=O)C1CC2(CC(C(=O)[O-])C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [19, 8, 19, 33, 41, 41, 41, 41, 41, 41, 41, 1, 8, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 19, 19, 19, 33, 33, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 41 rigid atoms, others: [48, 45, 43, 49, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18, 21, 22, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 151 number of broken/clashed sets: 41 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517006 none CN(CC1CCC[N@@H+](C)C1)C(=O)C1CC2(CC(C(=O)[O-])C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 28, 28, 41, 41, 41, 41, 41, 41, 41, 41, 41, 13, 13, 13, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41] 41 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 39, 34, 38, 28, 29, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 141 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517006 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517006 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 1: /scratch/stefan/7774842/working/building/REAL300004517006/1.* 0: /scratch/stefan/7774842/working/building/REAL300004517006/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517006 Building REAL300004517007 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517007' /scratch/stefan/7774842/working/building/REAL300004517007 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004517007 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517007/0 /scratch/stefan/7774842/working/building/REAL300004517007 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 13) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/13 `/scratch/stefan/7774842/working/3D/13' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)[O-])=NC(C(=O)N(C)CC2CCC[N@H+](C)C2)=C1) `REAL300004517007.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517007/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517007 none COC1=CC(C(=O)[O-])=NC(C(=O)N(C)CC2CCC[N@H+](C)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 4] 4 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 43, 44, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 45]) total number of confs: 19 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517007 none COC1=CC(C(=O)[O-])=NC(C(=O)N(C)CC2CCC[N@H+](C)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 1, 2, 2, 2, 1, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1] 4 rigid atoms, others: [1, 2, 3, 4, 5, 8, 9, 10, 45, 23, 27] set([0, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 19 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517007 /scratch/stefan/7774842/working /scratch/stefan/7774842 mkdir: created directory `1' /scratch/stefan/7774842/working/building/REAL300004517007/1 /scratch/stefan/7774842/working/building/REAL300004517007 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 1 (index: 14) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/14 `/scratch/stefan/7774842/working/3D/14' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)[O-])=NC(C(=O)N(C)CC2CCC[N@@H+](C)C2)=C1) `REAL300004517007.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004517007.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517007/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517007 none COC1=CC(C(=O)[O-])=NC(C(=O)N(C)CC2CCC[N@@H+](C)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 26, 26, 23, 18, 23, 9, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 18, 18, 18, 9, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 26] 26 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 43, 44, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 40, 41, 42, 45]) total number of confs: 89 number of broken/clashed sets: 26 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517007 none COC1=CC(C(=O)[O-])=NC(C(=O)N(C)CC2CCC[N@@H+](C)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 16, 16, 18, 26, 26, 26, 26, 26, 26, 26, 1, 2, 2, 2, 1, 16, 16, 16, 18, 18, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1] 26 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 45, 23, 27] set([0, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 85 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517007 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517007 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 1: /scratch/stefan/7774842/working/building/REAL300004517007/1.* 0: /scratch/stefan/7774842/working/building/REAL300004517007/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517007 Building REAL300004517008 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517008' /scratch/stefan/7774842/working/building/REAL300004517008 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004517008 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517008/0 /scratch/stefan/7774842/working/building/REAL300004517008 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 15) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/15 `/scratch/stefan/7774842/working/3D/15' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCC[N@H+](C)C1)C(=O)C1=CC=C(CCC(=O)[O-])C=C1) `REAL300004517008.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517008/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517008 none CN(CC1CCC[N@H+](C)C1)C(=O)C1=CC=C(CCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 1, 1, 1, 1, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 9, 14, 16, 16, 16, 16, 16, 16, 16, 1, 5, 1, 1, 1, 1, 1, 4, 8, 11, 11, 1, 1, 9, 9, 9, 14, 14, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 4, 4, 8, 8, 1, 1] 29 rigid atoms, others: [48, 41, 42, 11, 13, 14, 15, 16, 17, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45, 46]) total number of confs: 98 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517008 none CN(CC1CCC[N@H+](C)C1)C(=O)C1=CC=C(CCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 1, 1, 1, 1, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 13, 13, 16, 16, 14, 14, 23, 29, 29, 29, 16, 16, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 16, 16, 23, 23, 29, 29, 16, 16] 29 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 39, 34, 40, 35, 29, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 139 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517008 /scratch/stefan/7774842/working /scratch/stefan/7774842 mkdir: created directory `1' /scratch/stefan/7774842/working/building/REAL300004517008/1 /scratch/stefan/7774842/working/building/REAL300004517008 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 1 (index: 16) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/16 `/scratch/stefan/7774842/working/3D/16' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCC[N@@H+](C)C1)C(=O)C1=CC=C(CCC(=O)[O-])C=C1) `REAL300004517008.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004517008.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517008/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517008 none CN(CC1CCC[N@@H+](C)C1)C(=O)C1=CC=C(CCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 1, 1, 1, 1, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 9, 14, 16, 16, 16, 16, 16, 16, 16, 1, 5, 1, 1, 1, 1, 1, 4, 8, 10, 10, 1, 1, 9, 9, 9, 14, 14, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 4, 4, 8, 8, 1, 1] 28 rigid atoms, others: [48, 41, 42, 11, 13, 14, 15, 16, 17, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45, 46]) total number of confs: 96 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517008 none CN(CC1CCC[N@@H+](C)C1)C(=O)C1=CC=C(CCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 1, 1, 1, 1, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 13, 13, 16, 16, 13, 14, 23, 28, 28, 28, 16, 16, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 16, 16, 23, 23, 28, 28, 16, 16] 28 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 39, 34, 40, 35, 29, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 135 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517008 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517008 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 1: /scratch/stefan/7774842/working/building/REAL300004517008/1.* 0: /scratch/stefan/7774842/working/building/REAL300004517008/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517008 Building REAL300004517009 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517009' /scratch/stefan/7774842/working/building/REAL300004517009 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004517009 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517009/0 /scratch/stefan/7774842/working/building/REAL300004517009 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 17) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/17 `/scratch/stefan/7774842/working/3D/17' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCC[N@H+](C)C1)C(=O)C1CC2(C1)C(C(=O)[O-])C2(F)F) `REAL300004517009.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517009/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517009 none CN(CC1CCC[N@H+](C)C1)C(=O)C1CC2(C1)C(C(=O)[O-])C2(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1] 3 rigid atoms, others: [45, 43, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18, 21, 22, 23, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 17 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517009 none CN(CC1CCC[N@H+](C)C1)C(=O)C1CC2(C1)C(C(=O)[O-])C2(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 3, 3, 3, 3, 3, 3] 3 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 39, 34, 40, 35, 29, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 41, 42, 43, 44, 45, 46]) total number of confs: 16 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517009 /scratch/stefan/7774842/working /scratch/stefan/7774842 mkdir: created directory `1' /scratch/stefan/7774842/working/building/REAL300004517009/1 /scratch/stefan/7774842/working/building/REAL300004517009 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 1 (index: 18) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/18 `/scratch/stefan/7774842/working/3D/18' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCC[N@@H+](C)C1)C(=O)C1CC2(C1)C(C(=O)[O-])C2(F)F) `REAL300004517009.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004517009.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517009/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517009 none CN(CC1CCC[N@@H+](C)C1)C(=O)C1CC2(C1)C(C(=O)[O-])C2(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 3, 4, 4, 4, 4, 4, 4, 4, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1] 4 rigid atoms, others: [45, 43, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18, 21, 22, 23, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 19 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517009 none CN(CC1CCC[N@@H+](C)C1)C(=O)C1CC2(C1)C(C(=O)[O-])C2(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 4, 4, 4, 4, 4, 4] 4 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 39, 34, 40, 35, 29, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 41, 42, 43, 44, 45, 46]) total number of confs: 20 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517009 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517009 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 1: /scratch/stefan/7774842/working/building/REAL300004517009/1.* 0: /scratch/stefan/7774842/working/building/REAL300004517009/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517009 Building REAL300004517010 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517010' /scratch/stefan/7774842/working/building/REAL300004517010 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004517010 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517010/0 /scratch/stefan/7774842/working/building/REAL300004517010 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 19) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/19 `/scratch/stefan/7774842/working/3D/19' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)N(C)CC2CCC[N@H+](C)C2)C=C(C(=O)[O-])S1) `REAL300004517010.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517010/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517010 none CC1=C(C(=O)N(C)CC2CCC[N@H+](C)C2)C=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 6, 9, 5, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 6, 6, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 9] 9 rigid atoms, others: [32, 33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 14, 15, 40, 41, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 42]) total number of confs: 36 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517010 none CC1=C(C(=O)N(C)CC2CCC[N@H+](C)C2)C=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 5, 8, 8, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 2, 2, 1, 2, 2, 2, 8, 8, 8, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1] 9 rigid atoms, others: [0, 1, 2, 3, 42, 16, 17, 18, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 37 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517010 /scratch/stefan/7774842/working /scratch/stefan/7774842 mkdir: created directory `1' /scratch/stefan/7774842/working/building/REAL300004517010/1 /scratch/stefan/7774842/working/building/REAL300004517010 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 1 (index: 20) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/20 `/scratch/stefan/7774842/working/3D/20' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)N(C)CC2CCC[N@@H+](C)C2)C=C(C(=O)[O-])S1) `REAL300004517010.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004517010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517010/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517010 none CC1=C(C(=O)N(C)CC2CCC[N@@H+](C)C2)C=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 5, 8, 4, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 5, 5, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 8] 8 rigid atoms, others: [32, 33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 14, 15, 40, 41, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 42]) total number of confs: 33 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517010 none CC1=C(C(=O)N(C)CC2CCC[N@@H+](C)C2)C=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 5, 7, 7, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1] 8 rigid atoms, others: [0, 1, 2, 3, 42, 16, 17, 18, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 31 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517010 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517010 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 1: /scratch/stefan/7774842/working/building/REAL300004517010/1.* 0: /scratch/stefan/7774842/working/building/REAL300004517010/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517010 Building REAL300004517011 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517011' /scratch/stefan/7774842/working/building/REAL300004517011 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004517011 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517011/0 /scratch/stefan/7774842/working/building/REAL300004517011 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 21) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/21 `/scratch/stefan/7774842/working/3D/21' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCC[N@H+](C)C1)C(=O)C1=CC2=C(SC(C(=O)[O-])=C2)S1) `REAL300004517011.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517011/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517011 none CN(CC1CCC[N@H+](C)C1)C(=O)C1=CC2=C(SC(C(=O)[O-])=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 1, 1, 1, 1, 14, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [33, 11, 33, 63, 73, 73, 73, 73, 73, 73, 73, 1, 11, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 33, 33, 33, 63, 63, 73, 73, 73, 73, 73, 73, 73, 73, 73, 73, 73, 73, 1, 1] 73 rigid atoms, others: [41, 42, 11, 13, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 260 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517011 none CN(CC1CCC[N@H+](C)C1)C(=O)C1=CC2=C(SC(C(=O)[O-])=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 1, 1, 1, 1, 14, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [20, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 47, 47, 73, 73, 73, 73, 73, 73, 73, 73, 73, 73, 20, 20, 20, 9, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 73, 73] 73 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 39, 34, 40, 35, 29, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 41, 42]) total number of confs: 195 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517011 /scratch/stefan/7774842/working /scratch/stefan/7774842 mkdir: created directory `1' /scratch/stefan/7774842/working/building/REAL300004517011/1 /scratch/stefan/7774842/working/building/REAL300004517011 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 1 (index: 22) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/22 `/scratch/stefan/7774842/working/3D/22' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCC[N@@H+](C)C1)C(=O)C1=CC2=C(SC(C(=O)[O-])=C2)S1) `REAL300004517011.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004517011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517011/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517011 none CN(CC1CCC[N@@H+](C)C1)C(=O)C1=CC2=C(SC(C(=O)[O-])=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 1, 1, 1, 1, 14, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [34, 11, 34, 63, 73, 73, 73, 73, 73, 73, 73, 1, 11, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 34, 34, 34, 63, 63, 73, 73, 73, 73, 73, 73, 73, 73, 73, 73, 73, 73, 1, 1] 73 rigid atoms, others: [41, 42, 11, 13, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 258 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517011 none CN(CC1CCC[N@@H+](C)C1)C(=O)C1=CC2=C(SC(C(=O)[O-])=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 1, 1, 1, 1, 14, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [20, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 47, 47, 73, 73, 73, 73, 73, 73, 73, 73, 73, 73, 20, 20, 20, 9, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 73, 73] 73 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 39, 34, 40, 35, 29, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 41, 42]) total number of confs: 195 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517011 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517011 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 1: /scratch/stefan/7774842/working/building/REAL300004517011/1.* 0: /scratch/stefan/7774842/working/building/REAL300004517011/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517011 Building REAL300004517012 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517012' /scratch/stefan/7774842/working/building/REAL300004517012 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004517012 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517012/0 /scratch/stefan/7774842/working/building/REAL300004517012 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 23) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/23 `/scratch/stefan/7774842/working/3D/23' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)[O-])=C(Cl)C(C(=O)N(C)CC2CCC[N@H+](C)C2)=C1) `REAL300004517012.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517012/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517012 none COC1=CC(C(=O)[O-])=C(Cl)C(C(=O)N(C)CC2CCC[N@H+](C)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 16, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 27, 27, 27, 27, 27, 30, 30, 27, 27, 25, 16, 25, 8, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 30, 30, 30, 27, 16, 16, 16, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 27] 30 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 44, 45, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 46]) total number of confs: 107 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517012 none COC1=CC(C(=O)[O-])=C(Cl)C(C(=O)N(C)CC2CCC[N@H+](C)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 16, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [2, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 6, 6, 12, 12, 18, 27, 27, 27, 27, 27, 27, 27, 1, 3, 3, 3, 1, 12, 12, 12, 18, 18, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1] 30 rigid atoms, others: [1, 2, 3, 4, 5, 8, 9, 10, 11, 46, 24, 28] set([0, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517012 /scratch/stefan/7774842/working /scratch/stefan/7774842 mkdir: created directory `1' /scratch/stefan/7774842/working/building/REAL300004517012/1 /scratch/stefan/7774842/working/building/REAL300004517012 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 1 (index: 24) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/24 `/scratch/stefan/7774842/working/3D/24' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)[O-])=C(Cl)C(C(=O)N(C)CC2CCC[N@@H+](C)C2)=C1) `REAL300004517012.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004517012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517012/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517012 none COC1=CC(C(=O)[O-])=C(Cl)C(C(=O)N(C)CC2CCC[N@@H+](C)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 16, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 29, 29, 29, 29, 29, 31, 31, 29, 29, 26, 16, 26, 8, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 31, 31, 31, 29, 16, 16, 16, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 29] 31 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 44, 45, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43, 46]) total number of confs: 105 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517012 none COC1=CC(C(=O)[O-])=C(Cl)C(C(=O)N(C)CC2CCC[N@@H+](C)C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 16, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 6, 6, 14, 14, 20, 29, 29, 29, 29, 29, 29, 29, 1, 3, 3, 3, 1, 14, 14, 14, 20, 20, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1] 31 rigid atoms, others: [1, 2, 3, 4, 5, 8, 9, 10, 11, 46, 24, 28] set([0, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517012 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517012 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 1: /scratch/stefan/7774842/working/building/REAL300004517012/1.* 0: /scratch/stefan/7774842/working/building/REAL300004517012/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517012 Building REAL300004517013 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517013' /scratch/stefan/7774842/working/building/REAL300004517013 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004517013 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517013/0 /scratch/stefan/7774842/working/building/REAL300004517013 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 25) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/25 `/scratch/stefan/7774842/working/3D/25' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=CC(F)=C1C(=O)N(C)CC1CCC[N@H+](C)C1) `REAL300004517013.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517013/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517013 none CC1=C(C(=O)[O-])C=CC(F)=C1C(=O)N(C)CC1CCC[N@H+](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 21, 12, 21, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 12, 12, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1] 25 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 44, 45, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43]) total number of confs: 78 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517013 none CC1=C(C(=O)[O-])C=CC(F)=C1C(=O)N(C)CC1CCC[N@H+](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 4, 4, 12, 12, 22, 25, 25, 25, 25, 25, 25, 25, 2, 2, 2, 1, 1, 13, 13, 13, 22, 22, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25] 25 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 9, 10, 11, 27, 28] set([4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 106 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517013 /scratch/stefan/7774842/working /scratch/stefan/7774842 mkdir: created directory `1' /scratch/stefan/7774842/working/building/REAL300004517013/1 /scratch/stefan/7774842/working/building/REAL300004517013 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 1 (index: 26) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/26 `/scratch/stefan/7774842/working/3D/26' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=CC(F)=C1C(=O)N(C)CC1CCC[N@@H+](C)C1) `REAL300004517013.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004517013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517013/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517013 none CC1=C(C(=O)[O-])C=CC(F)=C1C(=O)N(C)CC1CCC[N@@H+](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 22, 13, 22, 6, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 13, 13, 13, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1] 26 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 44, 45, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43]) total number of confs: 81 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517013 none CC1=C(C(=O)[O-])C=CC(F)=C1C(=O)N(C)CC1CCC[N@@H+](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 5, 5, 13, 13, 24, 26, 26, 26, 26, 26, 26, 26, 2, 2, 2, 1, 1, 13, 13, 13, 24, 24, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26] 26 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 9, 10, 11, 27, 28] set([4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 104 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517013 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517013 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 1: /scratch/stefan/7774842/working/building/REAL300004517013/1.* 0: /scratch/stefan/7774842/working/building/REAL300004517013/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517013 Building REAL300004517014 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517014' /scratch/stefan/7774842/working/building/REAL300004517014 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004517014 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517014/0 /scratch/stefan/7774842/working/building/REAL300004517014 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 27) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/27 `/scratch/stefan/7774842/working/3D/27' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCC[N@H+](C)C1)C(=O)C1=CC2=C(C(=O)[O-])C=CC=C2S1) `REAL300004517014.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517014/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517014 none CN(CC1CCC[N@H+](C)C1)C(=O)C1=CC2=C(C(=O)[O-])C=CC=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 4, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1] 6 rigid atoms, others: [45, 43, 42, 11, 44, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 23 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517014 none CN(CC1CCC[N@H+](C)C1)C(=O)C1=CC2=C(C(=O)[O-])C=CC=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 6, 6, 6, 6] 6 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 40, 35, 41, 36, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 42, 43, 44, 45]) total number of confs: 27 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517014 /scratch/stefan/7774842/working /scratch/stefan/7774842 mkdir: created directory `1' /scratch/stefan/7774842/working/building/REAL300004517014/1 /scratch/stefan/7774842/working/building/REAL300004517014 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 1 (index: 28) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/28 `/scratch/stefan/7774842/working/3D/28' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCC[N@@H+](C)C1)C(=O)C1=CC2=C(C(=O)[O-])C=CC=C2S1) `REAL300004517014.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004517014.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517014/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517014 none CN(CC1CCC[N@@H+](C)C1)C(=O)C1=CC2=C(C(=O)[O-])C=CC=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 4, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1] 6 rigid atoms, others: [45, 43, 42, 11, 44, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 23 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517014 none CN(CC1CCC[N@@H+](C)C1)C(=O)C1=CC2=C(C(=O)[O-])C=CC=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 6, 6, 6, 6] 6 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 40, 35, 41, 36, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 42, 43, 44, 45]) total number of confs: 27 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517014 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517014 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 1: /scratch/stefan/7774842/working/building/REAL300004517014/1.* 0: /scratch/stefan/7774842/working/building/REAL300004517014/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517014 Building REAL300004517015 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517015' /scratch/stefan/7774842/working/building/REAL300004517015 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004517015 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517015/0 /scratch/stefan/7774842/working/building/REAL300004517015 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 29) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/29 `/scratch/stefan/7774842/working/3D/29' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCC[N@H+](C)C1)C(=O)CCC1=CC=CN=C1C(=O)[O-]) `REAL300004517015.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517015/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517015 none CN(CC1CCC[N@H+](C)C1)C(=O)CCC1=CC=CN=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 5, 5, 1, 1, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 4, 5, 4, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 4, 4, 1, 1, 1] 6 rigid atoms, others: [45, 14, 15, 16, 17, 18, 19, 20, 46, 47, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 27 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517015 none CN(CC1CCC[N@H+](C)C1)C(=O)CCC1=CC=CN=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 5, 5, 1, 1, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 5, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 6, 6, 6, 6, 6, 6, 6] 6 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 39, 34, 40, 35, 29, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 26 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517015 /scratch/stefan/7774842/working /scratch/stefan/7774842 mkdir: created directory `1' /scratch/stefan/7774842/working/building/REAL300004517015/1 /scratch/stefan/7774842/working/building/REAL300004517015 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 1 (index: 30) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/30 `/scratch/stefan/7774842/working/3D/30' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCC[N@@H+](C)C1)C(=O)CCC1=CC=CN=C1C(=O)[O-]) `REAL300004517015.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004517015.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517015/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517015 none CN(CC1CCC[N@@H+](C)C1)C(=O)CCC1=CC=CN=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 5, 5, 1, 1, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 4, 5, 4, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 5, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 4, 4, 1, 1, 1] 6 rigid atoms, others: [45, 14, 15, 16, 17, 18, 19, 20, 46, 47, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 27 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517015 none CN(CC1CCC[N@@H+](C)C1)C(=O)CCC1=CC=CN=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 5, 5, 1, 1, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 5, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 6, 6, 6, 6, 6, 6, 6] 6 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 39, 34, 40, 35, 29, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 26 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517015 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517015 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 1: /scratch/stefan/7774842/working/building/REAL300004517015/1.* 0: /scratch/stefan/7774842/working/building/REAL300004517015/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517015 Building REAL300004517016 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517016' /scratch/stefan/7774842/working/building/REAL300004517016 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004517016 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517016/0 /scratch/stefan/7774842/working/building/REAL300004517016 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 31) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/31 `/scratch/stefan/7774842/working/3D/31' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCC[N@H+](C)C1)C(=O)/C=C/C1=CC=C(C(=O)[O-])C=C1) `REAL300004517016.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517016/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517016 none CN(CC1CCC[N@H+](C)C1)C(=O)/C=C/C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [57, 19, 57, 118, 141, 141, 141, 141, 141, 141, 141, 4, 18, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57, 57, 57, 118, 118, 141, 141, 141, 141, 141, 141, 141, 141, 141, 141, 141, 141, 4, 4, 1, 1, 1, 1] 141 rigid atoms, others: [43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 521 number of broken/clashed sets: 36 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517016 none CN(CC1CCC[N@H+](C)C1)C(=O)/C=C/C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [20, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 59, 59, 141, 141, 141, 141, 141, 141, 141, 141, 141, 141, 20, 20, 20, 9, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 141, 141, 141, 141, 141, 141] 141 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 39, 34, 40, 35, 29, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 41, 42, 43, 44, 45, 46]) total number of confs: 412 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517016 /scratch/stefan/7774842/working /scratch/stefan/7774842 mkdir: created directory `1' /scratch/stefan/7774842/working/building/REAL300004517016/1 /scratch/stefan/7774842/working/building/REAL300004517016 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 1 (index: 32) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/32 `/scratch/stefan/7774842/working/3D/32' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCC[N@@H+](C)C1)C(=O)/C=C/C1=CC=C(C(=O)[O-])C=C1) `REAL300004517016.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004517016.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517016/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517016 none CN(CC1CCC[N@@H+](C)C1)C(=O)/C=C/C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [58, 19, 58, 119, 141, 141, 141, 141, 141, 141, 141, 4, 18, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 58, 58, 58, 119, 119, 141, 141, 141, 141, 141, 141, 141, 141, 141, 141, 141, 141, 4, 4, 1, 1, 1, 1] 141 rigid atoms, others: [43, 44, 45, 14, 15, 16, 17, 18, 19, 46, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 525 number of broken/clashed sets: 36 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517016 none CN(CC1CCC[N@@H+](C)C1)C(=O)/C=C/C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [20, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 60, 60, 141, 141, 141, 141, 141, 141, 141, 141, 141, 141, 20, 20, 20, 9, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 141, 141, 141, 141, 141, 141] 141 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 39, 34, 40, 35, 29, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 41, 42, 43, 44, 45, 46]) total number of confs: 412 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517016 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517016 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 1: /scratch/stefan/7774842/working/building/REAL300004517016/1.* 0: /scratch/stefan/7774842/working/building/REAL300004517016/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517016 Building REAL300004517017 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517017' /scratch/stefan/7774842/working/building/REAL300004517017 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004517017 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517017/0 /scratch/stefan/7774842/working/building/REAL300004517017 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 33) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/33 `/scratch/stefan/7774842/working/3D/33' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCC[N@H+](C)C1)C(=O)C1(C(=O)[O-])CC2(CCC2)C1) `REAL300004517017.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517017/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517017 none CN(CC1CCC[N@H+](C)C1)C(=O)C1(C(=O)[O-])CC2(CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 5, 1, 11, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 3 rigid atoms, others: [43, 49, 40, 41, 42, 11, 44, 13, 14, 45, 48, 17, 18, 19, 20, 21, 22, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 15 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517017 none CN(CC1CCC[N@H+](C)C1)C(=O)C1(C(=O)[O-])CC2(CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 5, 1, 11, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3] 3 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 39, 34, 38, 28, 29, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 16 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517017 /scratch/stefan/7774842/working /scratch/stefan/7774842 mkdir: created directory `1' /scratch/stefan/7774842/working/building/REAL300004517017/1 /scratch/stefan/7774842/working/building/REAL300004517017 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 1 (index: 34) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/34 `/scratch/stefan/7774842/working/3D/34' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCC[N@@H+](C)C1)C(=O)C1(C(=O)[O-])CC2(CCC2)C1) `REAL300004517017.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004517017.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517017/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517017 none CN(CC1CCC[N@@H+](C)C1)C(=O)C1(C(=O)[O-])CC2(CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 5, 1, 11, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 3, 6, 6, 6, 6, 6, 6, 6, 1, 2, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 6 rigid atoms, others: [43, 49, 40, 41, 42, 11, 44, 13, 14, 45, 48, 17, 18, 19, 20, 21, 22, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 27 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517017 none CN(CC1CCC[N@@H+](C)C1)C(=O)C1(C(=O)[O-])CC2(CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 5, 1, 11, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6] 6 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 39, 34, 38, 28, 29, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 26 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517017 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517017 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 1: /scratch/stefan/7774842/working/building/REAL300004517017/1.* 0: /scratch/stefan/7774842/working/building/REAL300004517017/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517017 Building REAL300004517018 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517018' /scratch/stefan/7774842/working/building/REAL300004517018 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004517018 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517018/0 /scratch/stefan/7774842/working/building/REAL300004517018 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 35) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/35 `/scratch/stefan/7774842/working/3D/35' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCC[N@H+](C)C1)C(=O)C1=CC2=C(N1)C(C(=O)[O-])=CS2) `REAL300004517018.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517018/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517018 none CN(CC1CCC[N@H+](C)C1)C(=O)C1=CC2=C(N1)C(C(=O)[O-])=CS2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 9, 10, 10, 10, 10, 10, 10, 10, 10, 1, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 9, 9, 9, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1] 10 rigid atoms, others: [43, 41, 42, 11, 13, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 33 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517018 none CN(CC1CCC[N@H+](C)C1)C(=O)C1=CC2=C(N1)C(C(=O)[O-])=CS2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 9, 9, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 7, 7, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 10, 10, 10] 10 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 39, 34, 40, 35, 29, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 41, 42, 43]) total number of confs: 39 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517018 /scratch/stefan/7774842/working /scratch/stefan/7774842 mkdir: created directory `1' /scratch/stefan/7774842/working/building/REAL300004517018/1 /scratch/stefan/7774842/working/building/REAL300004517018 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 1 (index: 36) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/36 `/scratch/stefan/7774842/working/3D/36' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCC[N@@H+](C)C1)C(=O)C1=CC2=C(N1)C(C(=O)[O-])=CS2) `REAL300004517018.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004517018.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517018/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517018 none CN(CC1CCC[N@@H+](C)C1)C(=O)C1=CC2=C(N1)C(C(=O)[O-])=CS2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [9, 6, 9, 10, 10, 10, 10, 10, 10, 10, 10, 1, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 9, 9, 9, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1] 10 rigid atoms, others: [43, 41, 42, 11, 13, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 33 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517018 none CN(CC1CCC[N@@H+](C)C1)C(=O)C1=CC2=C(N1)C(C(=O)[O-])=CS2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [7, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 9, 9, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 7, 7, 7, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 10, 10, 10] 10 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 39, 34, 40, 35, 29, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 41, 42, 43]) total number of confs: 39 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517018 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517018 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 1: /scratch/stefan/7774842/working/building/REAL300004517018/1.* 0: /scratch/stefan/7774842/working/building/REAL300004517018/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517018 Building REAL300004517019 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517019' /scratch/stefan/7774842/working/building/REAL300004517019 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004517019 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517019/0 /scratch/stefan/7774842/working/building/REAL300004517019 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 37) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/37 `/scratch/stefan/7774842/working/3D/37' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCC[N@H+](C)C1)C(=O)C1=CC2=C(C=C(C(=O)[O-])S2)N1) `REAL300004517019.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517019/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517019 none CN(CC1CCC[N@H+](C)C1)C(=O)C1=CC2=C(C=C(C(=O)[O-])S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [31, 11, 31, 59, 67, 67, 67, 67, 67, 67, 67, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 59, 59, 67, 67, 67, 67, 67, 67, 67, 67, 67, 67, 67, 67, 1, 1, 1] 67 rigid atoms, others: [43, 41, 42, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 250 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517019 none CN(CC1CCC[N@H+](C)C1)C(=O)C1=CC2=C(C=C(C(=O)[O-])S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [15, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 39, 39, 67, 67, 67, 67, 67, 67, 67, 67, 67, 67, 15, 15, 15, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 67, 67, 67] 67 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 39, 34, 40, 35, 29, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 41, 42, 43]) total number of confs: 174 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517019 /scratch/stefan/7774842/working /scratch/stefan/7774842 mkdir: created directory `1' /scratch/stefan/7774842/working/building/REAL300004517019/1 /scratch/stefan/7774842/working/building/REAL300004517019 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 1 (index: 38) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/38 `/scratch/stefan/7774842/working/3D/38' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCC[N@@H+](C)C1)C(=O)C1=CC2=C(C=C(C(=O)[O-])S2)N1) `REAL300004517019.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004517019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517019/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517019 none CN(CC1CCC[N@@H+](C)C1)C(=O)C1=CC2=C(C=C(C(=O)[O-])S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [31, 11, 31, 59, 67, 67, 67, 67, 67, 67, 67, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 59, 59, 67, 67, 67, 67, 67, 67, 67, 67, 67, 67, 67, 67, 1, 1, 1] 67 rigid atoms, others: [43, 41, 42, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 250 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517019 none CN(CC1CCC[N@@H+](C)C1)C(=O)C1=CC2=C(C=C(C(=O)[O-])S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [15, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 39, 39, 67, 67, 67, 67, 67, 67, 67, 67, 67, 67, 15, 15, 15, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 67, 67, 67] 67 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 39, 34, 40, 35, 29, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 41, 42, 43]) total number of confs: 174 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517019 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517019 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 1: /scratch/stefan/7774842/working/building/REAL300004517019/1.* 0: /scratch/stefan/7774842/working/building/REAL300004517019/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517019 Building REAL300004517020 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517020' /scratch/stefan/7774842/working/building/REAL300004517020 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004517020 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517020/0 /scratch/stefan/7774842/working/building/REAL300004517020 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 39) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/39 `/scratch/stefan/7774842/working/3D/39' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCC[N@H+](C)C1)C(=O)C1=CC2=C(N1)C(C(=O)[O-])=CO2) `REAL300004517020.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517020 none CN(CC1CCC[N@H+](C)C1)C(=O)C1=CC2=C(N1)C(C(=O)[O-])=CO2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 11, 13, 13, 13, 13, 13, 13, 13, 13, 1, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 11, 11, 11, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1] 13 rigid atoms, others: [43, 41, 42, 11, 13, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 45 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517020 none CN(CC1CCC[N@H+](C)C1)C(=O)C1=CC2=C(N1)C(C(=O)[O-])=CO2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 8, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 13, 13, 13] 13 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 39, 34, 40, 35, 29, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 41, 42, 43]) total number of confs: 51 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517020 /scratch/stefan/7774842/working /scratch/stefan/7774842 mkdir: created directory `1' /scratch/stefan/7774842/working/building/REAL300004517020/1 /scratch/stefan/7774842/working/building/REAL300004517020 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 1 (index: 40) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/40 `/scratch/stefan/7774842/working/3D/40' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCC[N@@H+](C)C1)C(=O)C1=CC2=C(N1)C(C(=O)[O-])=CO2) `REAL300004517020.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004517020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517020/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517020 none CN(CC1CCC[N@@H+](C)C1)C(=O)C1=CC2=C(N1)C(C(=O)[O-])=CO2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [11, 8, 11, 13, 13, 13, 13, 13, 13, 13, 13, 1, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 11, 11, 11, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1] 13 rigid atoms, others: [43, 41, 42, 11, 13, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 45 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517020 none CN(CC1CCC[N@@H+](C)C1)C(=O)C1=CC2=C(N1)C(C(=O)[O-])=CO2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 12, 12, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 8, 8, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 13, 13, 13] 13 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 39, 34, 40, 35, 29, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 41, 42, 43]) total number of confs: 51 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517020 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517020 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 1: /scratch/stefan/7774842/working/building/REAL300004517020/1.* 0: /scratch/stefan/7774842/working/building/REAL300004517020/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517020 Building REAL300004517021 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517021' /scratch/stefan/7774842/working/building/REAL300004517021 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004517021 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517021/0 /scratch/stefan/7774842/working/building/REAL300004517021 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 41) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/41 `/scratch/stefan/7774842/working/3D/41' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=CC=C1C(=O)N(C)CC1CCC[N@H+](C)C1) `REAL300004517021.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517021/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517021 none CC1=C(C(=O)[O-])C=CC=C1C(=O)N(C)CC1CCC[N@H+](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 20, 20, 19, 12, 19, 6, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 12, 12, 12, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1] 20 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43]) total number of confs: 65 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517021 none CC1=C(C(=O)[O-])C=CC=C1C(=O)N(C)CC1CCC[N@H+](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 5, 5, 12, 12, 18, 20, 20, 20, 20, 20, 20, 20, 2, 2, 2, 1, 1, 1, 12, 12, 12, 18, 18, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20] 20 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 9, 10, 26, 27, 28] set([4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 81 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517021 /scratch/stefan/7774842/working /scratch/stefan/7774842 mkdir: created directory `1' /scratch/stefan/7774842/working/building/REAL300004517021/1 /scratch/stefan/7774842/working/building/REAL300004517021 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 1 (index: 42) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/42 `/scratch/stefan/7774842/working/3D/42' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=CC=C1C(=O)N(C)CC1CCC[N@@H+](C)C1) `REAL300004517021.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004517021.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517021/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517021 none CC1=C(C(=O)[O-])C=CC=C1C(=O)N(C)CC1CCC[N@@H+](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 20, 20, 19, 12, 19, 6, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 12, 12, 12, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1] 20 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 41, 42, 43]) total number of confs: 65 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517021 none CC1=C(C(=O)[O-])C=CC=C1C(=O)N(C)CC1CCC[N@@H+](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 5, 5, 12, 12, 18, 20, 20, 20, 20, 20, 20, 20, 2, 2, 2, 1, 1, 1, 12, 12, 12, 18, 18, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20] 20 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 9, 10, 26, 27, 28] set([4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 81 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517021 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517021 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 1: /scratch/stefan/7774842/working/building/REAL300004517021/1.* 0: /scratch/stefan/7774842/working/building/REAL300004517021/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517021 Building REAL300004517022 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517022' /scratch/stefan/7774842/working/building/REAL300004517022 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004517022 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517022/0 /scratch/stefan/7774842/working/building/REAL300004517022 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 43) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/43 `/scratch/stefan/7774842/working/3D/43' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCC[N@H+](C)C1)C(=O)C=CC1=CC=C(C(=O)[O-])N=C1) `REAL300004517022.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517022/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517022 none CN(CC1CCC[N@H+](C)C1)C(=O)C=CC1=CC=C(C(=O)[O-])N=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 36, 102, 183, 201, 201, 201, 201, 201, 201, 201, 5, 36, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 102, 102, 102, 183, 183, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 5, 5, 1, 1, 1] 201 rigid atoms, others: [43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 742 number of broken/clashed sets: 44 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517022 none CN(CC1CCC[N@H+](C)C1)C(=O)C=CC1=CC=C(C(=O)[O-])N=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 49, 49, 136, 136, 201, 201, 201, 201, 201, 201, 201, 201, 18, 18, 18, 9, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 136, 136, 201, 201, 201] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 39, 34, 40, 35, 29, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 41, 42, 43, 44, 45]) total number of confs: 522 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517022 /scratch/stefan/7774842/working /scratch/stefan/7774842 mkdir: created directory `1' /scratch/stefan/7774842/working/building/REAL300004517022/1 /scratch/stefan/7774842/working/building/REAL300004517022 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 1 (index: 44) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/44 `/scratch/stefan/7774842/working/3D/44' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCC[N@@H+](C)C1)C(=O)C=CC1=CC=C(C(=O)[O-])N=C1) `REAL300004517022.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004517022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517022/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517022 none CN(CC1CCC[N@@H+](C)C1)C(=O)C=CC1=CC=C(C(=O)[O-])N=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [104, 36, 104, 193, 201, 201, 201, 201, 201, 201, 201, 5, 36, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 104, 104, 104, 193, 193, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 5, 5, 1, 1, 1] 201 rigid atoms, others: [43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 743 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517022 none CN(CC1CCC[N@@H+](C)C1)C(=O)C=CC1=CC=C(C(=O)[O-])N=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 51, 51, 146, 146, 201, 201, 201, 201, 201, 201, 201, 201, 16, 16, 16, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 146, 146, 201, 201, 201] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 39, 34, 40, 35, 29, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 41, 42, 43, 44, 45]) total number of confs: 513 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517022 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517022 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 1: /scratch/stefan/7774842/working/building/REAL300004517022/1.* 0: /scratch/stefan/7774842/working/building/REAL300004517022/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517022 Building REAL300004517023 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517023' /scratch/stefan/7774842/working/building/REAL300004517023 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004517023 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517023/0 /scratch/stefan/7774842/working/building/REAL300004517023 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 45) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/45 `/scratch/stefan/7774842/working/3D/45' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCC[N@H+](C)C1)C(=O)[C@@H]1[C@H]2CC[C@H](O2)[C@@H]1C(=O)[O-]) `REAL300004517023.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517023/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517023 none CN(CC1CCC[N@H+](C)C1)C(=O)[C@@H]1[C@H]2CC[C@H](O2)[C@@H]1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 5, 7, 5, 7, 5, 5, 5, 7, 12, 5, 7, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1] 3 rigid atoms, others: [45, 11, 44, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 46, 47, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 13 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517023 none CN(CC1CCC[N@H+](C)C1)C(=O)[C@@H]1[C@H]2CC[C@H](O2)[C@@H]1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 5, 7, 5, 7, 5, 5, 5, 7, 12, 5, 7, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 3, 3, 3, 3] 3 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 43, 34, 35, 36, 38, 42, 37] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 44, 45, 46, 47]) total number of confs: 16 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517023 /scratch/stefan/7774842/working /scratch/stefan/7774842 mkdir: created directory `1' /scratch/stefan/7774842/working/building/REAL300004517023/1 /scratch/stefan/7774842/working/building/REAL300004517023 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 1 (index: 46) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/46 `/scratch/stefan/7774842/working/3D/46' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCC[N@@H+](C)C1)C(=O)[C@@H]1[C@H]2CC[C@H](O2)[C@@H]1C(=O)[O-]) `REAL300004517023.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004517023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517023/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517023 none CN(CC1CCC[N@@H+](C)C1)C(=O)[C@@H]1[C@H]2CC[C@H](O2)[C@@H]1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 5, 7, 5, 7, 5, 5, 5, 7, 12, 5, 7, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 3, 4, 5, 5, 5, 5, 5, 5, 5, 5, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1] 5 rigid atoms, others: [45, 11, 44, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 46, 47, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 23 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517023 none CN(CC1CCC[N@@H+](C)C1)C(=O)[C@@H]1[C@H]2CC[C@H](O2)[C@@H]1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 5, 7, 5, 7, 5, 5, 5, 7, 12, 5, 7, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 5, 5, 5, 5] 5 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 43, 34, 35, 36, 38, 42, 37] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 39, 40, 41, 44, 45, 46, 47]) total number of confs: 23 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517023 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517023 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 1: /scratch/stefan/7774842/working/building/REAL300004517023/1.* 0: /scratch/stefan/7774842/working/building/REAL300004517023/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517023 Building REAL300004517024 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517024' /scratch/stefan/7774842/working/building/REAL300004517024 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004517024 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517024/0 /scratch/stefan/7774842/working/building/REAL300004517024 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 47) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/47 `/scratch/stefan/7774842/working/3D/47' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCC[N@H+](C)C1)C(=O)C1=CC=CC2=C(C(=O)[O-])C=CC=C12) `REAL300004517024.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517024/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517024 none CN(CC1CCC[N@H+](C)C1)C(=O)C1=CC=CC2=C(C(=O)[O-])C=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [15, 7, 15, 31, 34, 34, 34, 34, 34, 34, 34, 1, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 15, 15, 15, 31, 31, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 1, 1, 1] 34 rigid atoms, others: [48, 45, 43, 11, 44, 13, 14, 15, 16, 17, 18, 19, 46, 22, 23, 24, 25, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 135 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517024 none CN(CC1CCC[N@H+](C)C1)C(=O)C1=CC=CC2=C(C(=O)[O-])C=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [12, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 24, 24, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 12, 12, 7, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 34, 34, 34, 34, 34, 34] 34 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 35, 41, 36, 42, 37, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 43, 44, 45, 46, 47, 48]) total number of confs: 102 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517024 /scratch/stefan/7774842/working /scratch/stefan/7774842 mkdir: created directory `1' /scratch/stefan/7774842/working/building/REAL300004517024/1 /scratch/stefan/7774842/working/building/REAL300004517024 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 1 (index: 48) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/48 `/scratch/stefan/7774842/working/3D/48' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCC[N@@H+](C)C1)C(=O)C1=CC=CC2=C(C(=O)[O-])C=CC=C12) `REAL300004517024.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004517024.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517024/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517024 none CN(CC1CCC[N@@H+](C)C1)C(=O)C1=CC=CC2=C(C(=O)[O-])C=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 11, 17, 17, 17, 17, 17, 17, 17, 17, 1, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 11, 11, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [48, 45, 43, 11, 44, 13, 14, 15, 16, 17, 18, 19, 46, 22, 23, 24, 25, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 68 number of broken/clashed sets: 17 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517024 none CN(CC1CCC[N@@H+](C)C1)C(=O)C1=CC=CC2=C(C(=O)[O-])C=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 13, 13, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 35, 41, 36, 42, 37, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 38, 39, 40, 43, 44, 45, 46, 47, 48]) total number of confs: 57 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517024 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517024 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 1: /scratch/stefan/7774842/working/building/REAL300004517024/1.* 0: /scratch/stefan/7774842/working/building/REAL300004517024/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517024 Building REAL300004517025 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517025' /scratch/stefan/7774842/working/building/REAL300004517025 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004517025 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517025/0 /scratch/stefan/7774842/working/building/REAL300004517025 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 49) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/49 `/scratch/stefan/7774842/working/3D/49' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1CC(=O)N(C)CC1CCC[N@H+](C)C1) `REAL300004517025.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517025/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517025 none CC1=CC(C(=O)[O-])=CC=C1CC(=O)N(C)CC1CCC[N@H+](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 9, 8, 9, 4, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 8, 8, 8, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1] 10 rigid atoms, others: [48, 37, 38, 39, 40, 41, 42, 43, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46]) total number of confs: 41 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517025 none CC1=CC(C(=O)[O-])=CC=C1CC(=O)N(C)CC1CCC[N@H+](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 6, 6, 9, 9, 10, 10, 10, 10, 10, 10, 10, 10, 2, 2, 2, 1, 1, 1, 5, 5, 9, 9, 9, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 10 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517025 /scratch/stefan/7774842/working /scratch/stefan/7774842 mkdir: created directory `1' /scratch/stefan/7774842/working/building/REAL300004517025/1 /scratch/stefan/7774842/working/building/REAL300004517025 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 1 (index: 50) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/50 `/scratch/stefan/7774842/working/3D/50' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1CC(=O)N(C)CC1CCC[N@@H+](C)C1) `REAL300004517025.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004517025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517025/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517025 none CC1=CC(C(=O)[O-])=CC=C1CC(=O)N(C)CC1CCC[N@@H+](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 10, 9, 10, 4, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1] 11 rigid atoms, others: [48, 37, 38, 39, 40, 41, 42, 43, 15, 16, 17, 18, 19, 20, 21, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 44, 45, 46]) total number of confs: 43 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517025 none CC1=CC(C(=O)[O-])=CC=C1CC(=O)N(C)CC1CCC[N@@H+](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 9, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 5, 6, 6, 9, 9, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 1, 5, 5, 9, 9, 9, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 11 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517025 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517025 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 1: /scratch/stefan/7774842/working/building/REAL300004517025/1.* 0: /scratch/stefan/7774842/working/building/REAL300004517025/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517025 Building REAL300004517026 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517026' /scratch/stefan/7774842/working/building/REAL300004517026 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004517026 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517026/0 /scratch/stefan/7774842/working/building/REAL300004517026 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 51) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/51 `/scratch/stefan/7774842/working/3D/51' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCC[N@H+](C)C1)C(=O)CC1=CC(C(=O)[O-])=CS1) `REAL300004517026.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517026/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517026 none CN(CC1CCC[N@H+](C)C1)C(=O)CC1=CC(C(=O)[O-])=CS1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 5, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 2, 3, 1, 1, 1, 1, 1, 2, 2, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 1, 1] 3 rigid atoms, others: [41, 42, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 15 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517026 none CN(CC1CCC[N@H+](C)C1)C(=O)CC1=CC(C(=O)[O-])=CS1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 5, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 3, 3, 3, 3] 3 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 38, 37, 27, 28, 29, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 34, 35, 36, 39, 40, 41, 42]) total number of confs: 17 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517026 /scratch/stefan/7774842/working /scratch/stefan/7774842 mkdir: created directory `1' /scratch/stefan/7774842/working/building/REAL300004517026/1 /scratch/stefan/7774842/working/building/REAL300004517026 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 1 (index: 52) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/52 `/scratch/stefan/7774842/working/3D/52' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCC[N@@H+](C)C1)C(=O)CC1=CC(C(=O)[O-])=CS1) `REAL300004517026.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004517026.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517026/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517026 none CN(CC1CCC[N@@H+](C)C1)C(=O)CC1=CC(C(=O)[O-])=CS1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 5, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 3, 2, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 1, 1] 3 rigid atoms, others: [41, 42, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 11 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517026 none CN(CC1CCC[N@@H+](C)C1)C(=O)CC1=CC(C(=O)[O-])=CS1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 5, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 3, 3, 3, 3] 3 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 38, 37, 27, 28, 29, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 34, 35, 36, 39, 40, 41, 42]) total number of confs: 17 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517026 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517026 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 1: /scratch/stefan/7774842/working/building/REAL300004517026/1.* 0: /scratch/stefan/7774842/working/building/REAL300004517026/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517026 Building REAL300004517027 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517027' /scratch/stefan/7774842/working/building/REAL300004517027 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004517027 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517027/0 /scratch/stefan/7774842/working/building/REAL300004517027 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 53) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/53 `/scratch/stefan/7774842/working/3D/53' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCC[N@H+](C)C1)C(=O)CC1=CC=C(C(=O)[O-])C(F)=C1) `REAL300004517027.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517027/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517027 none CN(CC1CCC[N@H+](C)C1)C(=O)CC1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 5, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [19, 16, 19, 27, 28, 28, 28, 28, 28, 28, 28, 5, 16, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 19, 19, 19, 27, 27, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 5, 5, 1, 1, 1] 28 rigid atoms, others: [45, 43, 44, 13, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 114 number of broken/clashed sets: 28 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517027 none CN(CC1CCC[N@H+](C)C1)C(=O)CC1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 5, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 11, 11, 16, 28, 28, 28, 28, 28, 28, 28, 28, 28, 9, 9, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 16, 16, 28, 28, 28] 28 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 39, 34, 40, 35, 29, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 41, 42, 43, 44, 45]) total number of confs: 91 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517027 /scratch/stefan/7774842/working /scratch/stefan/7774842 mkdir: created directory `1' /scratch/stefan/7774842/working/building/REAL300004517027/1 /scratch/stefan/7774842/working/building/REAL300004517027 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 1 (index: 54) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/54 `/scratch/stefan/7774842/working/3D/54' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCC[N@@H+](C)C1)C(=O)CC1=CC=C(C(=O)[O-])C(F)=C1) `REAL300004517027.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004517027.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517027/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517027 none CN(CC1CCC[N@@H+](C)C1)C(=O)CC1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 5, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 10, 10, 10, 10, 10, 10, 10, 10, 3, 8, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 8, 8, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 1, 1, 1] 10 rigid atoms, others: [45, 43, 44, 13, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 42 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517027 none CN(CC1CCC[N@@H+](C)C1)C(=O)CC1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 5, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 4, 4, 4, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 6, 6, 10, 10, 10] 10 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 39, 34, 40, 35, 29, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 41, 42, 43, 44, 45]) total number of confs: 36 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517027 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517027 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 1: /scratch/stefan/7774842/working/building/REAL300004517027/1.* 0: /scratch/stefan/7774842/working/building/REAL300004517027/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517027 Building REAL300004517028 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517028' /scratch/stefan/7774842/working/building/REAL300004517028 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004517028 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517028/0 /scratch/stefan/7774842/working/building/REAL300004517028 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 55) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/55 `/scratch/stefan/7774842/working/3D/55' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCC[N@H+](C)C1)C(=O)C1=C2CCCCC2=C(C(=O)[O-])S1) `REAL300004517028.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517028/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517028 none CN(CC1CCC[N@H+](C)C1)C(=O)C1=C2CCCCC2=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 1, 1, 5, 5, 5, 5, 1, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [23, 9, 23, 40, 56, 56, 56, 56, 56, 56, 56, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 23, 23, 23, 40, 40, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56, 1, 1, 1, 1, 1, 1, 1, 1] 56 rigid atoms, others: [48, 45, 43, 49, 42, 11, 44, 13, 14, 15, 16, 17, 18, 19, 20, 46, 24, 47, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 205 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517028 none CN(CC1CCC[N@H+](C)C1)C(=O)C1=C2CCCCC2=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 1, 1, 5, 5, 5, 5, 1, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [17, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 35, 35, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56, 17, 17, 17, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 56, 56, 56, 56, 56, 56, 56, 56] 56 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 40, 35, 41, 36, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 151 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517028 /scratch/stefan/7774842/working /scratch/stefan/7774842 mkdir: created directory `1' /scratch/stefan/7774842/working/building/REAL300004517028/1 /scratch/stefan/7774842/working/building/REAL300004517028 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 1 (index: 56) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/56 `/scratch/stefan/7774842/working/3D/56' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCC[N@@H+](C)C1)C(=O)C1=C2CCCCC2=C(C(=O)[O-])S1) `REAL300004517028.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004517028.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517028/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517028 none CN(CC1CCC[N@@H+](C)C1)C(=O)C1=C2CCCCC2=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 1, 1, 5, 5, 5, 5, 1, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [22, 9, 22, 37, 53, 53, 53, 53, 53, 53, 53, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 22, 22, 22, 37, 37, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1, 1, 1, 1, 1, 1, 1, 1] 53 rigid atoms, others: [48, 45, 43, 49, 42, 11, 44, 13, 14, 15, 16, 17, 18, 19, 20, 46, 24, 47, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 188 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517028 none CN(CC1CCC[N@@H+](C)C1)C(=O)C1=C2CCCCC2=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 1, 1, 5, 5, 5, 5, 1, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [17, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 32, 32, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 53, 17, 17, 17, 8, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 53, 53, 53, 53, 53, 53, 53, 53] 53 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 34, 40, 35, 41, 36, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 140 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517028 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517028 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 1: /scratch/stefan/7774842/working/building/REAL300004517028/1.* 0: /scratch/stefan/7774842/working/building/REAL300004517028/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517028 Building REAL300004517029 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517029' /scratch/stefan/7774842/working/building/REAL300004517029 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004517029 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517029/0 /scratch/stefan/7774842/working/building/REAL300004517029 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 57) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/57 `/scratch/stefan/7774842/working/3D/57' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCC[N@H+](C)C1)C(=O)C12CCC(C(=O)[O-])(CC1)CC2) `REAL300004517029.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517029/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517029 none CN(CC1CCC[N@H+](C)C1)C(=O)C12CCC(C(=O)[O-])(CC1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 8, 10, 10, 10, 10, 10, 10, 10, 1, 4, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 4, 4, 4, 8, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 10 rigid atoms, others: [11, 13, 14, 15, 16, 17, 20, 21, 22, 23, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 36 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517029 none CN(CC1CCC[N@H+](C)C1)C(=O)C12CCC(C(=O)[O-])(CC1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 10 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 39, 34, 40, 35, 29, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 37 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517029 /scratch/stefan/7774842/working /scratch/stefan/7774842 mkdir: created directory `1' /scratch/stefan/7774842/working/building/REAL300004517029/1 /scratch/stefan/7774842/working/building/REAL300004517029 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 1 (index: 58) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/58 `/scratch/stefan/7774842/working/3D/58' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1CCC[N@@H+](C)C1)C(=O)C12CCC(C(=O)[O-])(CC1)CC2) `REAL300004517029.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004517029.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517029/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517029 none CN(CC1CCC[N@@H+](C)C1)C(=O)C12CCC(C(=O)[O-])(CC1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 9, 10, 10, 10, 10, 10, 10, 10, 1, 4, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 4, 4, 4, 9, 9, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 10 rigid atoms, others: [11, 13, 14, 15, 16, 17, 20, 21, 22, 23, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 43 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517029 none CN(CC1CCC[N@@H+](C)C1)C(=O)C12CCC(C(=O)[O-])(CC1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 5, 5, 9, 6, 5, 5, 1, 11, 5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 6, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10] 10 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 10, 39, 34, 40, 35, 29, 30, 31] set([0, 1, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 37 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517029 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517029 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 1: /scratch/stefan/7774842/working/building/REAL300004517029/1.* 0: /scratch/stefan/7774842/working/building/REAL300004517029/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517029 Building REAL300004517030 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517030' /scratch/stefan/7774842/working/building/REAL300004517030 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517030 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517030/0 /scratch/stefan/7774842/working/building/REAL300004517030 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 59) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/59 `/scratch/stefan/7774842/working/3D/59' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C1) `REAL300004517030.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517030.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517030/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517030 none O=C([O-])C1=CC=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 20, 31, 31, 20, 20, 20, 4, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 1, 1, 31, 31, 31, 31, 20, 4, 4, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 31, 31] 81 rigid atoms, others: [39, 40, 10, 11, 12, 13, 14, 15, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42]) total number of confs: 133 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517030 none O=C([O-])C1=CC=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 17, 31, 31, 17, 17, 81, 81, 81, 81, 31, 31, 1, 1, 1, 1, 4, 17, 17, 31, 31, 81, 72, 81, 81, 81, 81, 73, 81, 31, 31, 1, 1] 81 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 41, 42, 22, 23, 24, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 209 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517030 none O=C([O-])C1=CC=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 81, 60, 81, 81, 60, 60, 60, 19, 4, 3, 7, 7, 1, 1, 1, 1, 1, 1, 7, 7, 81, 81, 81, 81, 60, 19, 19, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 81, 81] 81 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 39, 40, 41, 42]) total number of confs: 340 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517030 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517030 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517030/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517030 Building REAL300004517031 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517031' /scratch/stefan/7774842/working/building/REAL300004517031 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517031 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517031/0 /scratch/stefan/7774842/working/building/REAL300004517031 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 60) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/60 `/scratch/stefan/7774842/working/3D/60' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=CC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=C1) `REAL300004517031.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517031.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517031/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517031 none O=C([O-])COC1=CC=CC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [124, 113, 124, 82, 35, 35, 35, 35, 35, 19, 19, 19, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 35, 113, 113, 35, 35, 35, 19, 3, 3, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 35] 201 rigid atoms, others: [34, 35, 45, 44, 13, 14, 15, 16, 17, 18, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 46]) total number of confs: 372 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517031 none O=C([O-])COC1=CC=CC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 14, 21, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 15, 35, 35, 15, 15, 84, 88, 88, 86, 35, 35, 1, 14, 14, 1, 1, 1, 3, 15, 15, 35, 35, 88, 84, 88, 88, 88, 88, 84, 88, 35, 35, 1] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 46, 25, 28, 29, 30] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 308 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517031 none O=C([O-])COC1=CC=CC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 170, 88, 88, 88, 88, 88, 54, 54, 54, 13, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 88, 201, 201, 88, 88, 88, 54, 13, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 88] 201 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 44, 45, 46]) total number of confs: 538 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517031 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517031 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517031/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517031 Building REAL300004517032 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517032' /scratch/stefan/7774842/working/building/REAL300004517032 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517032 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517032/0 /scratch/stefan/7774842/working/building/REAL300004517032 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 61) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/61 `/scratch/stefan/7774842/working/3D/61' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=C1) `REAL300004517032.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517032 none O=C([O-])C1=CC=CC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [44, 44, 44, 44, 44, 44, 44, 19, 19, 19, 5, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 1, 1, 44, 44, 44, 44, 19, 5, 5, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 44] 132 rigid atoms, others: [40, 41, 11, 12, 13, 14, 15, 16, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 42]) total number of confs: 100 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517032 none O=C([O-])C1=CC=CC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 25, 44, 44, 25, 40, 132, 132, 132, 132, 44, 44, 1, 1, 1, 1, 5, 25, 25, 44, 44, 132, 132, 132, 132, 132, 132, 121, 132, 44, 44, 1] 132 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 42, 23, 24, 25, 26] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 337 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517032 none O=C([O-])C1=CC=CC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 132 conformations in input total number of sets (complete confs): 132 using faster count positions algorithm for large data unique positions, atoms: [132, 132, 132, 132, 132, 132, 132, 73, 73, 73, 24, 3, 2, 9, 9, 1, 1, 1, 1, 1, 1, 9, 9, 132, 132, 132, 132, 73, 24, 24, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 132] 132 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 40, 41, 42]) total number of confs: 322 number of broken/clashed sets: 7 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517032 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517032 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517032/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517032 Building REAL300004517033 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517033' /scratch/stefan/7774842/working/building/REAL300004517033 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517033 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517033/0 /scratch/stefan/7774842/working/building/REAL300004517033 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 62) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/62 `/scratch/stefan/7774842/working/3D/62' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)S1) `REAL300004517033.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517033.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517033/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517033 none O=C([O-])C1=CC=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 14, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [61, 60, 61, 60, 60, 60, 23, 23, 23, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 60, 60, 60, 23, 4, 4, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1] 147 rigid atoms, others: [38, 39, 10, 11, 12, 13, 14, 15, 20, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 120 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517033 none O=C([O-])C1=CC=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 14, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 12, 12, 12, 40, 60, 60, 40, 40, 137, 147, 147, 138, 60, 60, 1, 1, 1, 12, 40, 40, 60, 60, 147, 137, 147, 147, 147, 147, 137, 147, 60, 60] 147 rigid atoms, others: [1, 3, 4, 5, 6, 7, 22, 23, 24] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 418 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517033 none O=C([O-])C1=CC=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 14, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [147, 147, 147, 147, 147, 147, 87, 87, 87, 17, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 147, 147, 147, 87, 17, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 147 rigid atoms, others: [32, 33, 34, 35, 36, 37, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 38, 39]) total number of confs: 332 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517033 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517033 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517033/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517033 Building REAL300004517034 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517034' /scratch/stefan/7774842/working/building/REAL300004517034 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517034 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517034/0 /scratch/stefan/7774842/working/building/REAL300004517034 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 63) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/63 `/scratch/stefan/7774842/working/3D/63' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=N1) `REAL300004517034.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517034.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517034/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517034 none O=C([O-])C1=CC=CC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 49, 49, 49, 49, 49, 27, 27, 27, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 1, 49, 49, 49, 49, 27, 4, 4, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1] 97 rigid atoms, others: [40, 41, 11, 12, 13, 14, 15, 16, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 115 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517034 none O=C([O-])C1=CC=CC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 23, 49, 49, 23, 23, 95, 97, 97, 93, 49, 49, 1, 1, 1, 1, 5, 23, 23, 49, 49, 96, 96, 97, 97, 97, 97, 93, 97, 49, 49] 97 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 23, 24, 25, 26] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 308 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517034 none O=C([O-])C1=CC=CC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [97, 97, 97, 97, 97, 97, 97, 95, 95, 95, 18, 4, 3, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 97, 97, 97, 97, 95, 18, 18, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 97 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 40, 41]) total number of confs: 258 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517034 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517034 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517034/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517034 Building REAL300004517035 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517035' /scratch/stefan/7774842/working/building/REAL300004517035 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517035 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517035/0 /scratch/stefan/7774842/working/building/REAL300004517035 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 64) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/64 `/scratch/stefan/7774842/working/3D/64' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(SC1=CC=CC=C1C(=O)NCC1=CC=C(N2CCCC2)C=C1)C(=O)[O-]) `REAL300004517035.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517035.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517035/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517035 none CC(SC1=CC=CC=C1C(=O)NCC1=CC=C(N2CCCC2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [84, 65, 44, 44, 44, 26, 44, 44, 16, 16, 16, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 84, 86, 86, 84, 84, 84, 84, 44, 44, 44, 44, 16, 3, 3, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1] 201 rigid atoms, others: [48, 49, 38, 39, 12, 13, 14, 15, 16, 17, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 310 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517035 none CC(SC1=CC=CC=C1C(=O)NCC1=CC=C(N2CCCC2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 7, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 30, 44, 44, 30, 30, 112, 123, 123, 112, 44, 44, 12, 13, 13, 12, 12, 12, 12, 1, 1, 1, 1, 9, 30, 30, 44, 44, 113, 114, 123, 123, 123, 123, 112, 115, 44, 44] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 34, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 344 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517035 none CC(SC1=CC=CC=C1C(=O)NCC1=CC=C(N2CCCC2)C=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 167, 123, 123, 123, 82, 123, 123, 59, 59, 59, 13, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201, 201, 201, 201, 201, 201, 123, 123, 123, 123, 59, 13, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 201 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 48, 49]) total number of confs: 736 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517035 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517035 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517035/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517035 Building REAL300004517036 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517036' /scratch/stefan/7774842/working/building/REAL300004517036 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517036 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517036/0 /scratch/stefan/7774842/working/building/REAL300004517036 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 65) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/65 `/scratch/stefan/7774842/working/3D/65' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=CC=C1OCC(=O)[O-]) `REAL300004517036.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517036.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517036/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517036 none CCOC1=CC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 35, 19, 19, 19, 8, 8, 8, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 19, 19, 19, 19, 70, 106, 120, 120, 39, 39, 39, 39, 39, 19, 8, 4, 4, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 19, 19, 106, 106] 201 rigid atoms, others: [38, 39, 9, 10, 11, 12, 13, 14, 48, 49, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 50, 51, 52, 53]) total number of confs: 433 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517036 none CCOC1=CC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 3, 1, 1, 1, 1, 1, 5, 5, 5, 15, 19, 19, 15, 17, 41, 41, 41, 41, 19, 19, 1, 1, 1, 1, 7, 17, 29, 29, 5, 5, 5, 5, 5, 1, 5, 15, 15, 19, 19, 41, 41, 41, 41, 41, 41, 41, 41, 19, 19, 1, 1, 17, 17] 201 rigid atoms, others: [34, 3, 4, 5, 6, 2, 50, 51, 21, 22, 23, 24] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 52, 53]) total number of confs: 226 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517036 none CCOC1=CC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [76, 72, 41, 41, 41, 17, 17, 17, 9, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 41, 41, 41, 41, 137, 201, 201, 201, 76, 76, 76, 76, 76, 41, 17, 9, 9, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 41, 41, 201, 201] 201 rigid atoms, others: [45, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 48, 49, 50, 51, 52, 53]) total number of confs: 680 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517036 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517036 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517036/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517036 Building REAL300004517037 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517037' /scratch/stefan/7774842/working/building/REAL300004517037 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517037 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517037/0 /scratch/stefan/7774842/working/building/REAL300004517037 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 66) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/66 `/scratch/stefan/7774842/working/3D/66' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(CCC(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C1) `REAL300004517037.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517037.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517037/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517037 none O=C([O-])C1=CC=C(CCC(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 13, 7, 7, 7, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 7, 3, 3, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 13, 13] 26 rigid atoms, others: [45, 35, 36, 12, 13, 14, 15, 16, 17, 46, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48]) total number of confs: 56 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517037 none O=C([O-])C1=CC=C(CCC(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 2, 5, 9, 9, 9, 12, 17, 17, 12, 12, 26, 27, 27, 27, 17, 17, 1, 1, 1, 1, 2, 2, 5, 5, 9, 12, 12, 17, 17, 26, 26, 27, 27, 27, 27, 27, 27, 17, 17, 1, 1] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 47, 48, 24, 25, 26, 27] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517037 none O=C([O-])C1=CC=C(CCC(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 26, 17, 17, 17, 13, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 26, 26, 26, 26, 26, 26, 26, 26, 17, 13, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 26, 26] 26 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 45, 46, 47, 48]) total number of confs: 106 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517037 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517037 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517037/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517037 Building REAL300004517038 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517038' /scratch/stefan/7774842/working/building/REAL300004517038 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517038 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517038/0 /scratch/stefan/7774842/working/building/REAL300004517038 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 67) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/67 `/scratch/stefan/7774842/working/3D/67' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=CC=N1) `REAL300004517038.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517038.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517038/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517038 none O=C([O-])C1=CC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=CC=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 8, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 45, 45, 45, 19, 19, 19, 5, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 45, 45, 45, 45, 19, 5, 5, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 45, 45] 130 rigid atoms, others: [38, 39, 9, 10, 11, 12, 13, 14, 19, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41]) total number of confs: 101 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517038 none O=C([O-])C1=CC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=CC=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 8, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 5, 5, 5, 25, 45, 45, 25, 40, 130, 130, 130, 130, 45, 45, 1, 1, 1, 1, 5, 25, 25, 45, 45, 130, 127, 130, 130, 130, 130, 120, 130, 45, 45, 1, 1] 130 rigid atoms, others: [1, 3, 4, 5, 6, 40, 41, 21, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 347 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517038 none O=C([O-])C1=CC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=CC=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 8, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [130, 130, 130, 130, 130, 70, 70, 70, 23, 4, 3, 8, 8, 1, 1, 1, 1, 1, 1, 8, 8, 130, 130, 130, 130, 70, 23, 23, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 130, 130] 130 rigid atoms, others: [32, 33, 34, 35, 36, 37, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 38, 39, 40, 41]) total number of confs: 318 number of broken/clashed sets: 7 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517038 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517038 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517038/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517038 Building REAL300004517039 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517039' /scratch/stefan/7774842/working/building/REAL300004517039 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517039 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517039/0 /scratch/stefan/7774842/working/building/REAL300004517039 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 68) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/68 `/scratch/stefan/7774842/working/3D/68' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=CC(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C1) `REAL300004517039.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517039.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517039/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517039 none O=C([O-])C1=CC=C(C=CC(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [122, 102, 122, 101, 122, 122, 100, 97, 25, 25, 25, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 122, 122, 122, 122, 102, 102, 25, 4, 4, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 122, 122] 201 rigid atoms, others: [33, 34, 44, 43, 12, 13, 14, 15, 16, 17, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46]) total number of confs: 465 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517039 none O=C([O-])C1=CC=C(C=CC(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 21, 21, 21, 74, 121, 121, 74, 89, 201, 201, 201, 201, 121, 121, 1, 1, 1, 1, 4, 4, 21, 74, 74, 121, 121, 201, 201, 201, 201, 201, 201, 198, 201, 121, 121, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 45, 46, 24, 25, 26, 27] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 647 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517039 none O=C([O-])C1=CC=C(C=CC(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 198, 194, 83, 83, 83, 17, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201, 201, 201, 201, 201, 83, 17, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201] 201 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 43, 44, 45, 46]) total number of confs: 598 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517039 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517039 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517039/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517039 Building REAL300004517040 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517040' /scratch/stefan/7774842/working/building/REAL300004517040 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517040 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517040/0 /scratch/stefan/7774842/working/building/REAL300004517040 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 69) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/69 `/scratch/stefan/7774842/working/3D/69' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=CC([N+](=O)[O-])=C1) `REAL300004517040.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517040.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517040/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517040 none O=C([O-])C1=CC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 8, 11, 11, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 67, 67, 26, 26, 26, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 67, 67, 67, 67, 67, 67, 67, 26, 5, 5, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 67, 67] 163 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 19, 20, 41, 42, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44]) total number of confs: 132 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517040 none O=C([O-])C1=CC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 8, 11, 11, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 29, 67, 67, 29, 48, 163, 163, 163, 163, 67, 67, 1, 1, 1, 1, 1, 1, 1, 5, 29, 29, 67, 67, 163, 158, 163, 163, 163, 163, 148, 163, 67, 67, 1, 1] 163 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 43, 44, 21, 22, 23, 24, 25, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 453 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517040 none O=C([O-])C1=CC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 8, 11, 11, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [163, 163, 163, 163, 163, 84, 84, 84, 17, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 163, 163, 163, 163, 163, 163, 163, 84, 17, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 163, 163] 163 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 41, 42, 43, 44]) total number of confs: 356 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517040 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517040 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517040/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517040 Building REAL300004517041 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517041' /scratch/stefan/7774842/working/building/REAL300004517041 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517041 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517041/0 /scratch/stefan/7774842/working/building/REAL300004517041 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 70) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/70 `/scratch/stefan/7774842/working/3D/70' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=CC([N+](=O)[O-])=C1) `REAL300004517041.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517041.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517041/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517041 none O=C([O-])C1=CC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 8, 11, 11, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 67, 67, 26, 26, 26, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 67, 67, 67, 67, 67, 67, 67, 26, 5, 5, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 67, 67] 163 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 19, 20, 41, 42, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44]) total number of confs: 132 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517041 none O=C([O-])C1=CC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 8, 11, 11, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 29, 67, 67, 29, 48, 163, 163, 163, 163, 67, 67, 1, 1, 1, 1, 1, 1, 1, 5, 29, 29, 67, 67, 163, 158, 163, 163, 163, 163, 148, 163, 67, 67, 1, 1] 163 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 43, 44, 21, 22, 23, 24, 25, 26, 27] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 453 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517041 none O=C([O-])C1=CC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 8, 11, 11, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [163, 163, 163, 163, 163, 84, 84, 84, 17, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 163, 163, 163, 163, 163, 163, 163, 84, 17, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 163, 163] 163 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 41, 42, 43, 44]) total number of confs: 356 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517041 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517041 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517041/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517041 Building REAL300004517042 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517042' /scratch/stefan/7774842/working/building/REAL300004517042 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517042 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517042/0 /scratch/stefan/7774842/working/building/REAL300004517042 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 71) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/71 `/scratch/stefan/7774842/working/3D/71' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=NN(C2=CC=CC=C2)C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=C1) `REAL300004517042.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517042.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517042/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517042 none O=C([O-])C1=NN(C2=CC=CC=C2)C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 15, 70, 86, 86, 70, 70, 196, 201, 201, 197, 86, 86, 5, 1, 1, 1, 1, 1, 15, 70, 70, 86, 86, 198, 197, 201, 201, 201, 201, 196, 198, 86, 86, 5] 201 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 11, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 513 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517042 none O=C([O-])C1=NN(C2=CC=CC=C2)C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [197, 197, 197, 197, 197, 197, 197, 201, 201, 197, 201, 201, 57, 57, 57, 13, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 197, 201, 201, 197, 201, 201, 57, 13, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 197] 201 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 47, 48, 49]) total number of confs: 365 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517042 none O=C([O-])C1=NN(C2=CC=CC=C2)C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 5, 5, 1, 5, 5, 1, 1, 12, 12, 12, 65, 84, 84, 65, 65, 192, 197, 197, 191, 84, 84, 1, 5, 5, 1, 5, 5, 12, 65, 65, 84, 84, 194, 192, 197, 197, 197, 197, 191, 194, 84, 84, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 12, 13, 49, 28] set([0, 2, 7, 8, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 521 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517042 none O=C([O-])C1=NN(C2=CC=CC=C2)C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [84, 84, 84, 84, 84, 84, 84, 86, 86, 84, 86, 86, 18, 17, 18, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 84, 86, 86, 84, 86, 86, 17, 3, 3, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 84] 201 rigid atoms, others: [48, 37, 38, 47, 16, 17, 18, 19, 20, 21, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 49]) total number of confs: 145 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517042 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517042 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517042/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517042 Building REAL300004517043 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517043' /scratch/stefan/7774842/working/building/REAL300004517043 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517043 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517043/0 /scratch/stefan/7774842/working/building/REAL300004517043 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 72) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/72 `/scratch/stefan/7774842/working/3D/72' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)O1) `REAL300004517043.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517043.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517043/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517043 none O=C([O-])C1=CC=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [33, 33, 33, 33, 33, 33, 24, 24, 24, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 33, 33, 33, 24, 5, 5, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1] 85 rigid atoms, others: [38, 39, 10, 11, 12, 13, 14, 15, 20, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 83 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517043 none O=C([O-])C1=CC=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 8, 8, 22, 33, 33, 23, 32, 85, 85, 85, 85, 33, 33, 1, 1, 1, 8, 22, 22, 33, 33, 85, 83, 85, 85, 85, 85, 77, 85, 33, 33] 85 rigid atoms, others: [1, 3, 4, 5, 6, 7, 22, 23, 24] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 225 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517043 none O=C([O-])C1=CC=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [85, 85, 85, 85, 85, 85, 75, 75, 75, 17, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 85, 85, 85, 75, 17, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 85 rigid atoms, others: [32, 33, 34, 35, 36, 37, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 38, 39]) total number of confs: 228 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517043 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517043 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517043/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517043 Building REAL300004517044 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517044' /scratch/stefan/7774842/working/building/REAL300004517044 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517044 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517044/0 /scratch/stefan/7774842/working/building/REAL300004517044 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 73) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/73 `/scratch/stefan/7774842/working/3D/73' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC=C1CCC(=O)NCC1=CC=C(N2CCCC2)C=C1) `REAL300004517044.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517044.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517044/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517044 none O=C([O-])C1=CC=CC=C1CCC(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 15, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 17, 17, 17, 17, 17, 17, 15, 15, 5, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1] 59 rigid atoms, others: [48, 35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 24, 25, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 67 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517044 none O=C([O-])C1=CC=CC=C1CCC(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 13, 13, 13, 17, 17, 17, 17, 17, 59, 59, 59, 59, 17, 17, 1, 1, 1, 1, 5, 5, 5, 5, 13, 17, 17, 17, 17, 59, 59, 59, 59, 59, 59, 59, 59, 17, 17] 59 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 26, 27, 28, 29] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517044 none O=C([O-])C1=CC=CC=C1CCC(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 59, 59, 59, 59, 59, 59, 53, 21, 21, 21, 5, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 59, 59, 59, 59, 59, 59, 53, 53, 21, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 59 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 47, 48]) total number of confs: 223 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517044 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517044 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517044/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517044 Building REAL300004517045 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517045' /scratch/stefan/7774842/working/building/REAL300004517045 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517045 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517045/0 /scratch/stefan/7774842/working/building/REAL300004517045 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 74) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/74 `/scratch/stefan/7774842/working/3D/74' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=CC(C)=C1OCC(=O)[O-]) `REAL300004517045.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517045/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517045 none CC1=CC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=CC(C)=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 5, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 47, 15, 15, 15, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 47, 47, 47, 32, 45, 78, 92, 104, 104, 47, 47, 47, 47, 15, 3, 3, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 47, 47, 47, 47, 92, 92] 201 rigid atoms, others: [35, 36, 7, 8, 9, 10, 11, 12, 45, 46, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49, 50, 51, 52]) total number of confs: 351 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517045 none CC1=CC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=CC(C)=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 5, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 5, 27, 47, 47, 27, 27, 113, 115, 115, 113, 47, 47, 1, 1, 1, 1, 1, 2, 7, 16, 16, 2, 2, 2, 1, 5, 27, 27, 47, 47, 115, 113, 115, 115, 115, 115, 113, 115, 47, 47, 1, 2, 2, 2, 7, 7] 201 rigid atoms, others: [0, 1, 2, 3, 4, 47, 19, 20, 21, 22, 23, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52]) total number of confs: 357 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517045 none CC1=CC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=CC(C)=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 5, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [115, 115, 115, 43, 43, 43, 13, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 115, 115, 115, 78, 115, 184, 201, 201, 201, 115, 115, 115, 115, 43, 13, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 115, 115, 115, 115, 201, 201] 201 rigid atoms, others: [43, 37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 656 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517045 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517045 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517045/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517045 Building REAL300004517046 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517046' /scratch/stefan/7774842/working/building/REAL300004517046 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517046 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517046/0 /scratch/stefan/7774842/working/building/REAL300004517046 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 75) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/75 `/scratch/stefan/7774842/working/3D/75' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(CC(=O)NCC2=CC=C(N3CCCC3)C=C2)=CC=C1) `REAL300004517046.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517046/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517046 none O=C([O-])C1=CC(CC(=O)NCC2=CC=C(N3CCCC3)C=C2)=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 91, 91, 91, 54, 23, 23, 23, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 91, 91, 91, 91, 54, 54, 23, 4, 4, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 91, 91, 91] 201 rigid atoms, others: [32, 41, 10, 11, 12, 13, 14, 15, 20, 21, 42, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 275 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517046 none O=C([O-])C1=CC(CC(=O)NCC2=CC=C(N3CCCC3)C=C2)=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 7, 11, 11, 11, 49, 91, 91, 49, 49, 174, 201, 201, 174, 91, 91, 1, 1, 1, 1, 7, 7, 11, 49, 49, 91, 91, 182, 184, 201, 201, 201, 201, 188, 191, 91, 91, 1, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 43, 44, 45, 22, 23, 24, 25] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 688 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517046 none O=C([O-])C1=CC(CC(=O)NCC2=CC=C(N3CCCC3)C=C2)=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 142, 79, 79, 79, 14, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201, 201, 201, 142, 142, 79, 14, 14, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201, 201] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 41, 42, 43, 44, 45]) total number of confs: 638 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517046 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517046 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517046/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517046 Building REAL300004517047 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517047' /scratch/stefan/7774842/working/building/REAL300004517047 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517047 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517047/0 /scratch/stefan/7774842/working/building/REAL300004517047 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 76) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/76 `/scratch/stefan/7774842/working/3D/76' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1CCCC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C1) `REAL300004517047.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517047.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517047/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517047 none O=C([O-])C1CCCC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [52, 43, 52, 43, 43, 43, 43, 25, 25, 25, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 43, 43, 43, 43, 43, 43, 43, 43, 43, 25, 4, 4, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 43, 43] 137 rigid atoms, others: [45, 35, 36, 11, 12, 13, 14, 15, 16, 21, 22, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48]) total number of confs: 170 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517047 none O=C([O-])C1CCCC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 18, 43, 43, 18, 18, 115, 137, 137, 114, 43, 43, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 18, 18, 43, 43, 131, 116, 137, 137, 137, 137, 117, 137, 43, 43, 1, 1] 137 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 47, 48, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 412 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517047 none O=C([O-])C1CCCC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [137, 137, 137, 137, 137, 137, 137, 93, 93, 93, 17, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 137, 137, 137, 137, 137, 137, 137, 137, 137, 93, 17, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 137, 137] 137 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 45, 46, 47, 48]) total number of confs: 416 number of broken/clashed sets: 8 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517047 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517047 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517047/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517047 Building REAL300004517048 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517048' /scratch/stefan/7774842/working/building/REAL300004517048 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517048 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517048/0 /scratch/stefan/7774842/working/building/REAL300004517048 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 77) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/77 `/scratch/stefan/7774842/working/3D/77' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C=N1) `REAL300004517048.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517048.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517048/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517048 none O=C([O-])C1=CC=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 59, 59, 59, 21, 21, 21, 4, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 59, 59, 59, 59, 21, 4, 4, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 59] 148 rigid atoms, others: [39, 40, 10, 11, 12, 13, 14, 15, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 41]) total number of confs: 118 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517048 none O=C([O-])C1=CC=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 7, 7, 7, 33, 59, 59, 33, 33, 132, 148, 148, 129, 59, 59, 1, 1, 1, 1, 7, 33, 33, 59, 59, 147, 132, 148, 148, 148, 148, 130, 148, 59, 59, 1] 148 rigid atoms, others: [1, 3, 4, 5, 6, 7, 41, 22, 23, 24, 25] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 477 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517048 none O=C([O-])C1=CC=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 148 conformations in input total number of sets (complete confs): 148 using faster count positions algorithm for large data unique positions, atoms: [148, 148, 148, 148, 148, 148, 67, 67, 67, 21, 4, 3, 8, 8, 1, 1, 1, 1, 1, 1, 8, 8, 148, 148, 148, 148, 67, 21, 21, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 148] 148 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 39, 40, 41]) total number of confs: 342 number of broken/clashed sets: 9 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517048 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517048 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517048/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517048 Building REAL300004517049 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517049' /scratch/stefan/7774842/working/building/REAL300004517049 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517049 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517049/0 /scratch/stefan/7774842/working/building/REAL300004517049 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 78) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/78 `/scratch/stefan/7774842/working/3D/78' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)N=C1) `REAL300004517049.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517049 none O=C([O-])C1=CC=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)N=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 8, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 32, 32, 32, 23, 23, 23, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 32, 32, 32, 32, 23, 5, 5, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 32] 78 rigid atoms, others: [39, 40, 10, 11, 12, 13, 14, 15, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 41]) total number of confs: 82 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517049 none O=C([O-])C1=CC=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)N=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 8, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 7, 7, 7, 19, 32, 32, 20, 25, 78, 78, 78, 78, 32, 32, 1, 1, 1, 1, 7, 19, 19, 32, 32, 78, 74, 78, 78, 78, 78, 73, 78, 32, 32, 1] 78 rigid atoms, others: [1, 3, 4, 5, 6, 7, 41, 22, 23, 24, 25] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 201 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517049 none O=C([O-])C1=CC=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)N=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 8, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [78, 78, 78, 78, 78, 78, 70, 70, 70, 17, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 78, 78, 78, 78, 70, 17, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 78] 78 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 39, 40, 41]) total number of confs: 212 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517049 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517049 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517049/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517049 Building REAL300004517050 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517050' /scratch/stefan/7774842/working/building/REAL300004517050 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517050 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517050/0 /scratch/stefan/7774842/working/building/REAL300004517050 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 79) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/79 `/scratch/stefan/7774842/working/3D/79' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CC(=O)[O-])CC(=O)NCC1=CC=C(N2CCCC2)C=C1) `REAL300004517050.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517050.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517050/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517050 none CC(C)(CC(=O)[O-])CC(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [197, 148, 197, 197, 201, 201, 201, 80, 80, 80, 15, 4, 4, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 197, 197, 197, 197, 197, 197, 201, 201, 148, 148, 80, 15, 15, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 201 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 46, 47]) total number of confs: 922 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517050 none CC(C)(CC(=O)[O-])CC(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [87, 45, 87, 87, 101, 115, 115, 24, 24, 24, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 1, 87, 87, 87, 87, 87, 87, 101, 101, 45, 45, 24, 5, 5, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1] 201 rigid atoms, others: [36, 37, 11, 12, 13, 14, 15, 16, 21, 22, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 529 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517050 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517050 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517050/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517050 Building REAL300004517051 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517051' /scratch/stefan/7774842/working/building/REAL300004517051 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517051 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517051/0 /scratch/stefan/7774842/working/building/REAL300004517051 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 80) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/80 `/scratch/stefan/7774842/working/3D/80' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C(F)=C1) `REAL300004517051.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517051.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517051/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517051 none O=C([O-])C1=CC=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [95, 95, 95, 44, 95, 95, 27, 27, 27, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 95, 95, 95, 95, 95, 27, 4, 4, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 95] 201 rigid atoms, others: [40, 41, 10, 11, 12, 13, 14, 15, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 42]) total number of confs: 334 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517051 none O=C([O-])C1=CC=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 57, 95, 95, 57, 57, 188, 201, 201, 189, 95, 95, 1, 1, 1, 1, 1, 12, 57, 57, 95, 95, 195, 191, 201, 201, 201, 201, 188, 200, 95, 95, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 42, 22, 23, 24, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 615 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517051 none O=C([O-])C1=CC=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 136, 201, 201, 85, 85, 85, 17, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201, 201, 201, 201, 85, 17, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 40, 41, 42]) total number of confs: 662 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517051 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517051 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517051/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517051 Building REAL300004517052 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517052' /scratch/stefan/7774842/working/building/REAL300004517052 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517052 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517052/0 /scratch/stefan/7774842/working/building/REAL300004517052 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 81) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/81 `/scratch/stefan/7774842/working/3D/81' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C=N1) `REAL300004517052.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517052/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517052 none O=C([O-])C1=CN=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 8, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 30, 30, 30, 23, 23, 23, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 30, 30, 30, 23, 5, 5, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 30] 72 rigid atoms, others: [38, 39, 10, 11, 12, 13, 14, 15, 20, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 40]) total number of confs: 79 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517052 none O=C([O-])C1=CN=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 8, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 5, 5, 5, 17, 30, 30, 17, 22, 72, 72, 72, 72, 30, 30, 1, 1, 1, 5, 17, 17, 30, 30, 72, 70, 72, 72, 72, 72, 65, 72, 30, 30, 1] 72 rigid atoms, others: [1, 3, 4, 5, 6, 7, 40, 22, 23, 24] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 192 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517052 none O=C([O-])C1=CN=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 8, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 72, 72, 72, 70, 70, 70, 17, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 72, 72, 72, 70, 17, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 72] 72 rigid atoms, others: [32, 33, 34, 35, 36, 37, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 38, 39, 40]) total number of confs: 202 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517052 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517052 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517052/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517052 Building REAL300004517053 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517053' /scratch/stefan/7774842/working/building/REAL300004517053 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517053 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517053/0 /scratch/stefan/7774842/working/building/REAL300004517053 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 82) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/82 `/scratch/stefan/7774842/working/3D/82' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])[C@H]1CC[C@H](C(=O)NCC2=CC=C(N3CCCC3)C=C2)CC1) `REAL300004517053.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517053.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517053/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517053 none O=C([O-])[C@H]1CC[C@H](C(=O)NCC2=CC=C(N3CCCC3)C=C2)CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [85, 78, 85, 78, 78, 78, 78, 23, 78, 23, 23, 4, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 1, 1, 78, 78, 78, 78, 78, 78, 23, 4, 4, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 78, 78, 78, 78] 201 rigid atoms, others: [33, 34, 44, 43, 12, 13, 14, 15, 16, 17, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47, 48]) total number of confs: 244 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517053 none O=C([O-])[C@H]1CC[C@H](C(=O)NCC2=CC=C(N3CCCC3)C=C2)CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 47, 78, 78, 47, 50, 201, 201, 201, 201, 78, 78, 1, 1, 1, 1, 1, 1, 12, 47, 47, 78, 78, 201, 186, 201, 201, 201, 201, 190, 201, 78, 78, 1, 1, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 45, 46, 47, 48, 24, 25, 26, 27, 28, 29] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 521 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517053 none O=C([O-])[C@H]1CC[C@H](C(=O)NCC2=CC=C(N3CCCC3)C=C2)CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 78, 201, 78, 78, 20, 4, 2, 7, 7, 1, 1, 1, 1, 1, 1, 7, 7, 201, 201, 201, 201, 201, 201, 78, 20, 20, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 201, 201, 201, 201] 201 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 43, 44, 45, 46, 47, 48]) total number of confs: 587 number of broken/clashed sets: 5 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517053 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517053 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517053/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517053 Building REAL300004517054 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517054' /scratch/stefan/7774842/working/building/REAL300004517054 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517054 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517054/0 /scratch/stefan/7774842/working/building/REAL300004517054 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 83) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/83 `/scratch/stefan/7774842/working/3D/83' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1CCC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)CC1) `REAL300004517054.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517054.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517054/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517054 none O=C([O-])C1CCC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [85, 78, 85, 78, 78, 78, 23, 23, 23, 4, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 1, 1, 78, 78, 78, 78, 78, 78, 78, 78, 23, 4, 4, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 78, 78, 78, 78] 201 rigid atoms, others: [33, 34, 43, 44, 10, 11, 12, 13, 14, 15, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47, 48]) total number of confs: 244 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517054 none O=C([O-])C1CCC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 12, 12, 12, 47, 78, 78, 47, 51, 201, 201, 201, 201, 78, 78, 1, 1, 1, 1, 1, 1, 1, 1, 12, 47, 47, 78, 78, 201, 186, 201, 201, 201, 201, 190, 201, 78, 78, 1, 1, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 45, 46, 47, 48, 22, 23, 24, 25, 26, 27, 28, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 522 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517054 none O=C([O-])C1CCC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 78, 78, 78, 20, 4, 4, 7, 7, 1, 1, 1, 1, 1, 1, 7, 7, 201, 201, 201, 201, 201, 201, 201, 201, 78, 20, 20, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 201, 201, 201, 201] 201 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 43, 44, 45, 46, 47, 48]) total number of confs: 583 number of broken/clashed sets: 5 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517054 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517054 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517054/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517054 Building REAL300004517055 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517055' /scratch/stefan/7774842/working/building/REAL300004517055 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517055 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517055/0 /scratch/stefan/7774842/working/building/REAL300004517055 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 84) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/84 `/scratch/stefan/7774842/working/3D/84' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(CC(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C1) `REAL300004517055.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517055.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517055/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517055 none O=C([O-])C1=CC=C(CC(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 77, 77, 77, 77, 49, 19, 19, 19, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 77, 77, 77, 77, 49, 49, 19, 3, 3, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 77, 77] 201 rigid atoms, others: [32, 33, 43, 42, 11, 12, 13, 14, 15, 16, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45]) total number of confs: 250 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517055 none O=C([O-])C1=CC=C(CC(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 11, 11, 11, 58, 100, 100, 58, 58, 186, 201, 201, 186, 100, 100, 1, 1, 1, 1, 6, 6, 11, 58, 58, 100, 100, 189, 190, 201, 201, 201, 201, 189, 194, 100, 100, 1, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 44, 45, 23, 24, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 638 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517055 none O=C([O-])C1=CC=C(CC(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 122, 69, 69, 69, 13, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201, 201, 201, 122, 122, 69, 13, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 42, 43, 44, 45]) total number of confs: 618 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517055 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517055 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517055/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517055 Building REAL300004517056 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517056' /scratch/stefan/7774842/working/building/REAL300004517056 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517056 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517056/0 /scratch/stefan/7774842/working/building/REAL300004517056 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 85) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/85 `/scratch/stefan/7774842/working/3D/85' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN(CC(=O)NCC2=CC=C(N3CCCC3)C=C2)N=N1) `REAL300004517056.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517056.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517056/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517056 none O=C([O-])C1=CN(CC(=O)NCC2=CC=C(N3CCCC3)C=C2)N=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 106, 106, 106, 62, 19, 19, 19, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 106, 106, 106, 62, 62, 19, 3, 3, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1] 201 rigid atoms, others: [40, 41, 10, 11, 12, 13, 14, 15, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 295 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517056 none O=C([O-])C1=CN(CC(=O)NCC2=CC=C(N3CCCC3)C=C2)N=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 8, 33, 33, 33, 77, 106, 106, 77, 77, 197, 201, 201, 197, 106, 106, 1, 1, 1, 8, 8, 33, 77, 77, 106, 106, 201, 197, 201, 201, 201, 201, 197, 201, 106, 106] 201 rigid atoms, others: [1, 3, 4, 5, 6, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 620 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517056 none O=C([O-])C1=CN(CC(=O)NCC2=CC=C(N3CCCC3)C=C2)N=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 142, 54, 54, 54, 13, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201, 201, 142, 142, 54, 13, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 40, 41]) total number of confs: 654 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517056 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517056 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517056/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517056 Building REAL300004517057 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517057' /scratch/stefan/7774842/working/building/REAL300004517057 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517057 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517057/0 /scratch/stefan/7774842/working/building/REAL300004517057 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 86) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/86 `/scratch/stefan/7774842/working/3D/86' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=CC=C1C(=O)[O-]) `REAL300004517057.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517057.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517057/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517057 none CC1=NC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 27, 27, 27, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 1, 1, 60, 60, 60, 60, 67, 67, 60, 60, 60, 27, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 60, 60] 140 rigid atoms, others: [32, 7, 8, 9, 10, 11, 12, 17, 18, 41, 42, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44]) total number of confs: 156 number of broken/clashed sets: 17 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517057 none CC1=NC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 7, 31, 60, 60, 31, 32, 132, 140, 140, 135, 60, 60, 1, 1, 1, 1, 3, 3, 2, 2, 2, 7, 31, 31, 60, 60, 140, 130, 140, 140, 140, 140, 132, 140, 60, 60, 1, 1] 140 rigid atoms, others: [0, 1, 2, 3, 4, 43, 44, 19, 20, 21, 22] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 401 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517057 none CC1=NC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [140, 140, 140, 98, 98, 98, 23, 4, 3, 7, 7, 1, 1, 1, 1, 1, 1, 7, 7, 140, 140, 140, 140, 140, 140, 140, 140, 140, 98, 23, 23, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 140, 140] 140 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 41, 42, 43, 44]) total number of confs: 355 number of broken/clashed sets: 17 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517057 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517057 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517057/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517057 Building REAL300004517058 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517058' /scratch/stefan/7774842/working/building/REAL300004517058 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517058 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517058/0 /scratch/stefan/7774842/working/building/REAL300004517058 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 87) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/87 `/scratch/stefan/7774842/working/3D/87' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C1) `REAL300004517058.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517058.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517058/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517058 none O=C([O-])C1=CC=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 20, 31, 31, 20, 20, 20, 4, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 1, 1, 31, 31, 31, 31, 20, 4, 4, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 31, 31] 81 rigid atoms, others: [39, 40, 10, 11, 12, 13, 14, 15, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42]) total number of confs: 133 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517058 none O=C([O-])C1=CC=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 17, 31, 31, 17, 17, 81, 81, 81, 81, 31, 31, 1, 1, 1, 1, 4, 17, 17, 31, 31, 81, 72, 81, 81, 81, 81, 73, 81, 31, 31, 1, 1] 81 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 41, 42, 22, 23, 24, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 209 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517058 none O=C([O-])C1=CC=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 81, 60, 81, 81, 60, 60, 60, 19, 4, 3, 7, 7, 1, 1, 1, 1, 1, 1, 7, 7, 81, 81, 81, 81, 60, 19, 19, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 81, 81] 81 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 39, 40, 41, 42]) total number of confs: 340 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517058 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517058 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517058/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517058 Building REAL300004517059 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517059' /scratch/stefan/7774842/working/building/REAL300004517059 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517059 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517059/0 /scratch/stefan/7774842/working/building/REAL300004517059 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 88) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/88 `/scratch/stefan/7774842/working/3D/88' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])[C@@H]1CC[C@H](C(=O)NCC2=CC=C(N3CCCC3)C=C2)C1) `REAL300004517059.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517059.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517059/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517059 none O=C([O-])[C@@H]1CC[C@H](C(=O)NCC2=CC=C(N3CCCC3)C=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [93, 81, 93, 81, 81, 81, 81, 25, 81, 25, 25, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 81, 81, 81, 81, 81, 25, 4, 4, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 81, 81] 201 rigid atoms, others: [32, 33, 42, 43, 12, 13, 14, 15, 16, 17, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45]) total number of confs: 272 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517059 none O=C([O-])[C@@H]1CC[C@H](C(=O)NCC2=CC=C(N3CCCC3)C=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 37, 81, 81, 37, 42, 201, 201, 201, 201, 81, 81, 1, 1, 1, 1, 1, 9, 37, 37, 81, 81, 201, 183, 201, 201, 201, 201, 188, 201, 81, 81, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 44, 45, 24, 25, 26, 27, 28] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 519 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517059 none O=C([O-])[C@@H]1CC[C@H](C(=O)NCC2=CC=C(N3CCCC3)C=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 80, 201, 80, 80, 14, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201, 201, 201, 201, 80, 14, 14, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 42, 43, 44, 45]) total number of confs: 583 number of broken/clashed sets: 10 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517059 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517059 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517059/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517059 Building REAL300004517060 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517060' /scratch/stefan/7774842/working/building/REAL300004517060 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517060 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517060/0 /scratch/stefan/7774842/working/building/REAL300004517060 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 89) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/89 `/scratch/stefan/7774842/working/3D/89' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=CC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=C1) `REAL300004517060.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517060/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517060 none O=C([O-])CC1=CC=CC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [109, 83, 109, 58, 58, 58, 58, 58, 26, 26, 26, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 58, 83, 83, 58, 58, 58, 26, 5, 5, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 58] 201 rigid atoms, others: [33, 34, 44, 43, 12, 13, 14, 15, 16, 17, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 45]) total number of confs: 373 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517060 none O=C([O-])CC1=CC=CC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 2, 7, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 26, 58, 58, 26, 38, 153, 153, 153, 153, 58, 58, 1, 2, 2, 1, 1, 1, 5, 26, 26, 58, 58, 153, 147, 153, 153, 153, 153, 140, 153, 58, 58, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 45, 24, 27, 28, 29] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 402 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517060 none O=C([O-])CC1=CC=CC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 153, 153, 153, 153, 153, 80, 80, 80, 14, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 153, 201, 201, 153, 153, 153, 80, 14, 14, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 153] 201 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 43, 44, 45]) total number of confs: 626 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517060 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517060 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517060/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517060 Building REAL300004517061 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517061' /scratch/stefan/7774842/working/building/REAL300004517061 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517061 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517061/0 /scratch/stefan/7774842/working/building/REAL300004517061 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 90) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/90 `/scratch/stefan/7774842/working/3D/90' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C=CO1) `REAL300004517061.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517061/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517061 none O=C([O-])CC1=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C=CO1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 78, 106, 67, 67, 21, 21, 21, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 67, 67, 67, 78, 78, 21, 3, 3, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 67, 67] 201 rigid atoms, others: [39, 40, 9, 10, 11, 12, 13, 14, 19, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42]) total number of confs: 294 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517061 none O=C([O-])CC1=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C=CO1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 3, 7, 1, 1, 1, 1, 10, 10, 10, 36, 67, 67, 36, 36, 151, 185, 185, 151, 67, 67, 1, 1, 1, 3, 3, 10, 36, 36, 67, 67, 162, 156, 185, 185, 185, 185, 152, 169, 67, 67, 1, 1] 201 rigid atoms, others: [3, 4, 5, 6, 41, 42, 21, 22, 23] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 570 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517061 none O=C([O-])CC1=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C=CO1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 185, 185, 77, 77, 77, 13, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 185, 185, 185, 201, 201, 77, 13, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 185, 185] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 39, 40, 41, 42]) total number of confs: 474 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517061 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517061 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517061/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517061 Building REAL300004517062 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517062' /scratch/stefan/7774842/working/building/REAL300004517062 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517062 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517062/0 /scratch/stefan/7774842/working/building/REAL300004517062 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 91) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/91 `/scratch/stefan/7774842/working/3D/91' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=COC(CC(=O)[O-])=C1C(=O)NCC1=CC=C(N2CCCC2)C=C1) `REAL300004517062.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517062.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517062/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517062 none CC1=COC(CC(=O)[O-])=C1C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 5, 1, 11, 11, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [69, 68, 68, 68, 68, 69, 69, 95, 95, 19, 19, 19, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 69, 69, 69, 68, 69, 69, 19, 3, 3, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1] 164 rigid atoms, others: [34, 35, 45, 44, 13, 14, 15, 16, 17, 18, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 225 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517062 none CC1=COC(CC(=O)[O-])=C1C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 5, 1, 11, 11, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 8, 8, 8, 44, 69, 69, 45, 45, 151, 164, 164, 151, 69, 69, 2, 2, 2, 1, 3, 3, 9, 44, 44, 69, 69, 164, 151, 164, 164, 164, 164, 151, 164, 69, 69] 164 rigid atoms, others: [0, 1, 2, 3, 4, 5, 9, 10, 28] set([6, 7, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 494 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517062 none CC1=COC(CC(=O)[O-])=C1C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 5, 1, 11, 11, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [164, 164, 164, 164, 164, 164, 164, 164, 164, 69, 69, 69, 13, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 164, 164, 164, 164, 164, 164, 69, 13, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 164 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 44, 45]) total number of confs: 337 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517062 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517062 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517062/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517062 Building REAL300004517063 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517063' /scratch/stefan/7774842/working/building/REAL300004517063 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517063 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517063/0 /scratch/stefan/7774842/working/building/REAL300004517063 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 92) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/92 `/scratch/stefan/7774842/working/3D/92' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=NC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=C1) `REAL300004517063.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517063/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517063 none O=C([O-])C1=CC=NC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [79, 78, 79, 78, 78, 78, 78, 25, 25, 25, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 1, 78, 78, 78, 25, 4, 4, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 78] 201 rigid atoms, others: [39, 40, 11, 12, 13, 14, 15, 16, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 41]) total number of confs: 147 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517063 none O=C([O-])C1=CC=NC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 47, 78, 78, 47, 47, 187, 201, 201, 185, 78, 78, 1, 1, 1, 9, 47, 47, 78, 78, 201, 186, 201, 201, 201, 201, 182, 201, 78, 78, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 41, 23, 24, 25] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 587 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517063 none O=C([O-])C1=CC=NC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 98, 98, 98, 18, 4, 3, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 201, 201, 201, 98, 18, 18, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 39, 40, 41]) total number of confs: 423 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517063 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517063 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517063/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517063 Building REAL300004517064 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517064' /scratch/stefan/7774842/working/building/REAL300004517064 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517064 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517064/0 /scratch/stefan/7774842/working/building/REAL300004517064 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 93) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/93 `/scratch/stefan/7774842/working/3D/93' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C12CC(C(=O)NCC3=CC=C(N4CCCC4)C=C3)(C1)C2) `REAL300004517064.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517064 none O=C([O-])C12CC(C(=O)NCC3=CC=C(N4CCCC4)C=C3)(C1)C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [73, 61, 73, 61, 61, 25, 25, 25, 4, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 1, 1, 61, 61, 61, 61, 25, 4, 4, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 61, 61, 61, 61] 106 rigid atoms, others: [38, 39, 9, 10, 11, 12, 13, 14, 19, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 173 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517064 none O=C([O-])C12CC(C(=O)NCC3=CC=C(N4CCCC4)C=C3)(C1)C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 6, 6, 6, 31, 61, 61, 31, 32, 106, 106, 106, 105, 61, 61, 1, 1, 1, 1, 6, 31, 31, 61, 61, 106, 94, 106, 106, 106, 106, 101, 106, 61, 61, 1, 1, 1, 1] 106 rigid atoms, others: [1, 3, 4, 5, 6, 40, 41, 42, 43, 21, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 355 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517064 none O=C([O-])C12CC(C(=O)NCC3=CC=C(N4CCCC4)C=C3)(C1)C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 106, 106, 106, 84, 84, 84, 20, 4, 4, 7, 7, 1, 1, 1, 1, 1, 1, 7, 7, 106, 106, 106, 106, 84, 20, 20, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 106, 106, 106, 106] 106 rigid atoms, others: [32, 33, 34, 35, 36, 37, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 38, 39, 40, 41, 42, 43]) total number of confs: 283 number of broken/clashed sets: 8 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517064 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517064 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517064/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517064 Building REAL300004517065 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517065' /scratch/stefan/7774842/working/building/REAL300004517065 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517065 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517065/0 /scratch/stefan/7774842/working/building/REAL300004517065 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 94) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/94 `/scratch/stefan/7774842/working/3D/94' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1(C(=O)NCC2=CC=C(N3CCCC3)C=C2)CCC1) `REAL300004517065.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517065.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517065/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517065 none O=C([O-])C1(C(=O)NCC2=CC=C(N3CCCC3)C=C2)CCC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [103, 66, 103, 25, 25, 25, 4, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 1, 1, 66, 66, 66, 25, 4, 4, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 66, 66, 66, 66, 66, 66] 201 rigid atoms, others: [35, 36, 7, 8, 9, 10, 11, 12, 17, 18, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42]) total number of confs: 348 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517065 none O=C([O-])C1(C(=O)NCC2=CC=C(N3CCCC3)C=C2)CCC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 4, 4, 4, 22, 66, 66, 22, 22, 162, 201, 201, 160, 66, 66, 1, 1, 1, 4, 22, 22, 66, 66, 175, 168, 201, 201, 201, 201, 165, 197, 66, 66, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 3, 4, 37, 38, 39, 40, 41, 42, 19, 20, 21] set([0, 2, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 667 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517065 none O=C([O-])C1(C(=O)NCC2=CC=C(N3CCCC3)C=C2)CCC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 98, 98, 98, 19, 4, 2, 7, 7, 1, 1, 1, 1, 1, 1, 7, 7, 201, 201, 201, 98, 19, 19, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [32, 33, 34, 11, 12, 13, 14, 15, 16, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 620 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517065 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517065 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517065/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517065 Building REAL300004517066 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517066' /scratch/stefan/7774842/working/building/REAL300004517066 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517066 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517066/0 /scratch/stefan/7774842/working/building/REAL300004517066 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 95) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/95 `/scratch/stefan/7774842/working/3D/95' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1CCC(CC(=O)NCC2=CC=C(N3CCCC3)C=C2)CC1) `REAL300004517066.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517066/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517066 none O=C([O-])C1CCC(CC(=O)NCC2=CC=C(N3CCCC3)C=C2)CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [111, 89, 111, 89, 89, 89, 71, 19, 19, 19, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 89, 89, 89, 89, 89, 89, 89, 89, 71, 71, 19, 3, 3, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 89, 89, 89, 89] 201 rigid atoms, others: [36, 37, 11, 12, 13, 14, 15, 16, 21, 22, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 48, 49, 50, 51]) total number of confs: 404 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517066 none O=C([O-])C1CCC(CC(=O)NCC2=CC=C(N3CCCC3)C=C2)CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 6, 19, 19, 19, 53, 89, 89, 53, 62, 201, 201, 201, 201, 89, 89, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 19, 53, 53, 89, 89, 201, 193, 201, 201, 201, 201, 193, 201, 89, 89, 1, 1, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 48, 49, 50, 51, 23, 24, 25, 26, 27, 28, 29, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 565 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517066 none O=C([O-])C1CCC(CC(=O)NCC2=CC=C(N3CCCC3)C=C2)CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 185, 59, 59, 59, 13, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201, 201, 201, 201, 201, 201, 201, 185, 185, 59, 13, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201, 201, 201] 201 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 46, 47, 48, 49, 50, 51]) total number of confs: 741 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517066 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517066 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517066/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517066 Building REAL300004517067 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517067' /scratch/stefan/7774842/working/building/REAL300004517067 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517067 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517067/0 /scratch/stefan/7774842/working/building/REAL300004517067 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 96) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/96 `/scratch/stefan/7774842/working/3D/96' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C12CCC(C(=O)NCC3=CC=C(N4CCCC4)C=C3)(CC1)C2) `REAL300004517067.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517067 none O=C([O-])C12CCC(C(=O)NCC3=CC=C(N4CCCC4)C=C3)(CC1)C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [82, 68, 82, 68, 68, 68, 22, 22, 22, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 68, 68, 68, 68, 68, 68, 68, 22, 4, 4, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 68, 68, 68, 68, 68, 68] 201 rigid atoms, others: [32, 33, 43, 10, 11, 12, 13, 14, 15, 20, 21, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46, 47, 48, 49]) total number of confs: 179 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517067 none O=C([O-])C12CCC(C(=O)NCC3=CC=C(N4CCCC4)C=C3)(CC1)C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 7, 7, 7, 32, 68, 68, 32, 39, 201, 201, 201, 201, 68, 68, 1, 1, 1, 1, 1, 1, 1, 7, 32, 32, 68, 68, 201, 188, 201, 201, 201, 201, 186, 201, 68, 68, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 44, 45, 46, 47, 48, 49, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 491 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517067 none O=C([O-])C12CCC(C(=O)NCC3=CC=C(N4CCCC4)C=C3)(CC1)C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 76, 76, 76, 14, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201, 201, 201, 201, 201, 201, 76, 14, 14, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 382 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517067 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517067 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517067/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517067 Building REAL300004517068 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517068' /scratch/stefan/7774842/working/building/REAL300004517068 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517068 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517068/0 /scratch/stefan/7774842/working/building/REAL300004517068 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 97) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/97 `/scratch/stefan/7774842/working/3D/97' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C12CCC(C(=O)NCC3=CC=C(N4CCCC4)C=C3)(CC1)CC2) `REAL300004517068.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517068/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517068 none O=C([O-])C12CCC(C(=O)NCC3=CC=C(N4CCCC4)C=C3)(CC1)CC2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [82, 27, 82, 27, 77, 77, 27, 27, 27, 4, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 1, 1, 77, 77, 77, 77, 77, 77, 77, 77, 27, 4, 4, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 77, 77, 77, 77, 77, 77, 77, 77] 116 rigid atoms, others: [33, 34, 43, 44, 10, 11, 12, 13, 14, 15, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 496 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517068 none O=C([O-])C12CCC(C(=O)NCC3=CC=C(N4CCCC4)C=C3)(CC1)CC2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 6, 6, 6, 31, 77, 77, 31, 34, 110, 116, 116, 116, 77, 77, 1, 1, 1, 1, 1, 1, 1, 1, 6, 31, 31, 77, 77, 116, 108, 116, 116, 116, 116, 112, 116, 77, 77, 1, 1, 1, 1, 1, 1, 1, 1] 116 rigid atoms, others: [1, 3, 4, 5, 6, 7, 22, 23, 24, 25, 26, 27, 28, 29, 45, 46, 47, 48, 49, 50, 51, 52] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 424 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517068 none O=C([O-])C12CCC(C(=O)NCC3=CC=C(N4CCCC4)C=C3)(CC1)CC2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [116, 101, 116, 101, 116, 116, 101, 101, 101, 21, 4, 2, 7, 7, 1, 1, 1, 1, 1, 1, 7, 7, 116, 116, 116, 116, 116, 116, 116, 116, 101, 21, 21, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 116, 116, 116, 116, 116, 116, 116, 116] 116 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 443 number of broken/clashed sets: 9 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517068 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517068 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517068/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517068 Building REAL300004517069 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517069' /scratch/stefan/7774842/working/building/REAL300004517069 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517069 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517069/0 /scratch/stefan/7774842/working/building/REAL300004517069 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 98) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/98 `/scratch/stefan/7774842/working/3D/98' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CC(=O)[O-])CC(=O)NCC1=CC=C(N2CCCC2)C=C1) `REAL300004517069.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517069 none CC(C)(CC(=O)[O-])CC(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [197, 148, 197, 197, 201, 201, 201, 80, 80, 80, 15, 4, 4, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 197, 197, 197, 197, 197, 197, 201, 201, 148, 148, 80, 15, 15, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 201 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 46, 47]) total number of confs: 922 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517069 none CC(C)(CC(=O)[O-])CC(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [87, 45, 87, 87, 101, 115, 115, 24, 24, 24, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 1, 87, 87, 87, 87, 87, 87, 101, 101, 45, 45, 24, 5, 5, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1] 201 rigid atoms, others: [36, 37, 11, 12, 13, 14, 15, 16, 21, 22, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 529 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517069 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517069 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517069/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517069 Building REAL300004517070 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517070' /scratch/stefan/7774842/working/building/REAL300004517070 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517070 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517070/0 /scratch/stefan/7774842/working/building/REAL300004517070 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 99) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/99 `/scratch/stefan/7774842/working/3D/99' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(=O)[O-])CC(=O)NCC1=CC=C(N2CCCC2)C=C1) `REAL300004517070.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517070 none CC(CC(=O)[O-])CC(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 11, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [183, 147, 183, 201, 201, 201, 70, 70, 70, 13, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 183, 183, 183, 183, 201, 201, 147, 147, 70, 13, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 201 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 43, 44]) total number of confs: 882 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517070 none CC(CC(=O)[O-])CC(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 11, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [86, 56, 86, 107, 119, 119, 20, 20, 20, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 86, 86, 86, 86, 107, 107, 56, 56, 20, 4, 4, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1] 201 rigid atoms, others: [33, 34, 43, 44, 10, 11, 12, 13, 14, 15, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 548 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517070 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517070 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517070/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517070 Building REAL300004517071 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517071' /scratch/stefan/7774842/working/building/REAL300004517071 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517071 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517071/0 /scratch/stefan/7774842/working/building/REAL300004517071 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 100) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/100 `/scratch/stefan/7774842/working/3D/100' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C2N=CC=C(C(=O)NCC3=CC=C(N4CCCC4)C=C3)N2N=C1) `REAL300004517071.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517071 none O=C([O-])C1=C2N=CC=C(C(=O)NCC3=CC=C(N4CCCC4)C=C3)N2N=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 8, 8, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 67, 67, 67, 67, 67, 22, 22, 22, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 67, 67, 67, 67, 67, 22, 5, 5, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 67] 188 rigid atoms, others: [32, 33, 42, 43, 12, 13, 14, 15, 16, 17, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 44]) total number of confs: 127 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517071 none O=C([O-])C1=C2N=CC=C(C(=O)NCC3=CC=C(N4CCCC4)C=C3)N2N=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 8, 8, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 38, 67, 67, 39, 50, 188, 188, 188, 188, 67, 67, 1, 1, 1, 1, 1, 8, 38, 38, 67, 67, 188, 183, 188, 188, 188, 188, 177, 188, 67, 67, 1] 188 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 44, 24, 25, 26, 27, 28] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 459 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517071 none O=C([O-])C1=C2N=CC=C(C(=O)NCC3=CC=C(N4CCCC4)C=C3)N2N=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 8, 8, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [188, 188, 188, 188, 188, 188, 188, 188, 79, 79, 79, 17, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 188, 188, 188, 188, 188, 79, 17, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 188] 188 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 42, 43, 44]) total number of confs: 382 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517071 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517071 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517071/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517071 Building REAL300004517072 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517072' /scratch/stefan/7774842/working/building/REAL300004517072 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517072 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517072/0 /scratch/stefan/7774842/working/building/REAL300004517072 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 101) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/101 `/scratch/stefan/7774842/working/3D/101' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)NC2=CC=CC=C21) `REAL300004517072.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517072/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517072 none O=C([O-])CC1=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)NC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [55, 50, 55, 50, 50, 21, 21, 21, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 4, 4, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 50, 50, 50, 50, 50] 142 rigid atoms, others: [33, 34, 43, 9, 10, 11, 12, 13, 14, 44, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49]) total number of confs: 125 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517072 none O=C([O-])CC1=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)NC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [7, 2, 7, 1, 1, 1, 1, 7, 7, 7, 23, 50, 50, 23, 23, 109, 142, 142, 109, 50, 50, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 23, 23, 50, 50, 110, 109, 142, 142, 142, 142, 109, 114, 50, 50, 1, 1, 1, 1, 1] 142 rigid atoms, others: [3, 4, 5, 6, 45, 46, 47, 48, 49, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 407 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517072 none O=C([O-])CC1=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)NC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [142, 142, 142, 142, 142, 73, 73, 73, 17, 4, 3, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 142, 142, 142, 142, 142, 142, 142, 142, 142, 73, 17, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 142, 142, 142, 142, 142] 142 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 319 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517072 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517072 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517072/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517072 Building REAL300004517073 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517073' /scratch/stefan/7774842/working/building/REAL300004517073 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517073 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517073/0 /scratch/stefan/7774842/working/building/REAL300004517073 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 102) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/102 `/scratch/stefan/7774842/working/3D/102' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=NO1) `REAL300004517073.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517073.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517073/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517073 none O=C([O-])C1=CC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=NO1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 8, 12, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 136 conformations in input total number of sets (complete confs): 136 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 52, 52, 52, 22, 22, 22, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 52, 52, 52, 22, 4, 4, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1] 136 rigid atoms, others: [37, 38, 9, 10, 11, 12, 13, 14, 19, 20, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 109 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517073 none O=C([O-])C1=CC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=NO1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 8, 12, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 136 conformations in input total number of sets (complete confs): 136 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 11, 11, 11, 34, 52, 52, 34, 34, 127, 136, 136, 131, 52, 52, 1, 1, 1, 11, 34, 34, 52, 52, 136, 124, 136, 136, 136, 136, 126, 136, 52, 52] 136 rigid atoms, others: [1, 3, 4, 5, 6, 21, 22, 23] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 364 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517073 none O=C([O-])C1=CC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=NO1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 8, 12, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 136 conformations in input total number of sets (complete confs): 136 using faster count positions algorithm for large data unique positions, atoms: [136, 136, 136, 136, 136, 79, 79, 79, 17, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 136, 136, 136, 79, 17, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 136 rigid atoms, others: [32, 33, 34, 35, 36, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 37, 38]) total number of confs: 320 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517073 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517073 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517073/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517073 Building REAL300004517074 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517074' /scratch/stefan/7774842/working/building/REAL300004517074 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517074 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517074/0 /scratch/stefan/7774842/working/building/REAL300004517074 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 103) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/103 `/scratch/stefan/7774842/working/3D/103' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1(C(=O)NCC2=CC=C(N3CCCC3)C=C2)CCCC1) `REAL300004517074.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517074.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517074/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517074 none O=C([O-])C1(C(=O)NCC2=CC=C(N3CCCC3)C=C2)CCCC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [111, 66, 111, 25, 25, 25, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 66, 66, 66, 66, 25, 4, 4, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 66, 66, 66, 66, 66, 66, 66, 66] 201 rigid atoms, others: [36, 37, 7, 8, 9, 10, 11, 12, 17, 18, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 374 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517074 none O=C([O-])C1(C(=O)NCC2=CC=C(N3CCCC3)C=C2)CCCC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 4, 4, 4, 22, 66, 66, 22, 23, 201, 201, 201, 201, 66, 66, 1, 1, 1, 1, 4, 22, 22, 66, 66, 201, 179, 201, 201, 201, 201, 175, 201, 66, 66, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 3, 4, 38, 39, 40, 41, 42, 43, 44, 45, 19, 20, 21, 22] set([0, 2, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 478 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517074 none O=C([O-])C1(C(=O)NCC2=CC=C(N3CCCC3)C=C2)CCCC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 93, 93, 93, 17, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201, 201, 201, 93, 17, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [32, 33, 34, 35, 11, 12, 13, 14, 15, 16, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 600 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517074 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517074 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517074/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517074 Building REAL300004517075 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517075' /scratch/stefan/7774842/working/building/REAL300004517075 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517075 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517075/0 /scratch/stefan/7774842/working/building/REAL300004517075 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 104) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/104 `/scratch/stefan/7774842/working/3D/104' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C2CCCC(CC(=O)NCC3=CC=C(N4CCCC4)C=C3)C2=C1) `REAL300004517075.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517075.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517075/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517075 none O=C([O-])C1=CC=C2CCCC(CC(=O)NCC3=CC=C(N4CCCC4)C=C3)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 3] 9 rigid atoms, others: [43, 44, 15, 16, 17, 18, 19, 20, 53, 54, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49, 50, 51, 52, 55]) total number of confs: 16 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517075 none O=C([O-])C1=CC=C2CCCC(CC(=O)NCC3=CC=C(N4CCCC4)C=C3)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3, 3, 3, 9, 9, 9, 9, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 3, 3, 3, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 1] 9 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 55] set([0, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 25 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517075 none O=C([O-])C1=CC=C2CCCC(CC(=O)NCC3=CC=C(N4CCCC4)C=C3)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 9] 9 rigid atoms, others: [51, 45, 46, 47, 48, 49, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 53, 54, 55]) total number of confs: 31 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517075 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517075 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517075/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517075 Building REAL300004517076 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517076' /scratch/stefan/7774842/working/building/REAL300004517076 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517076 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517076/0 /scratch/stefan/7774842/working/building/REAL300004517076 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 105) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/105 `/scratch/stefan/7774842/working/3D/105' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C(C(=O)[O-])O1) `REAL300004517076.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517076 none CC1=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [74, 74, 24, 24, 24, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 1, 1, 74, 74, 74, 74, 74, 74, 74, 74, 74, 24, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 74] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 16, 17, 41, 40, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 42]) total number of confs: 138 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517076 none CC1=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 10, 10, 10, 49, 74, 74, 49, 63, 201, 201, 201, 201, 74, 74, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 49, 49, 74, 74, 201, 199, 201, 201, 201, 201, 188, 201, 74, 74, 1] 201 rigid atoms, others: [0, 1, 2, 3, 42, 18, 19, 20, 21, 22, 23] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 526 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517076 none CC1=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 85, 85, 85, 21, 4, 3, 7, 7, 1, 1, 1, 1, 1, 1, 7, 7, 201, 201, 201, 201, 201, 201, 201, 201, 201, 85, 21, 21, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 40, 41, 42]) total number of confs: 412 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517076 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517076 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517076/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517076 Building REAL300004517077 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517077' /scratch/stefan/7774842/working/building/REAL300004517077 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517077 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517077/0 /scratch/stefan/7774842/working/building/REAL300004517077 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 106) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/106 `/scratch/stefan/7774842/working/3D/106' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])OC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=C1) `REAL300004517077.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517077/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517077 none CC1=C(C(=O)[O-])OC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 55, 55, 55, 55, 28, 28, 28, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 55, 55, 55, 55, 28, 5, 5, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 55] 167 rigid atoms, others: [40, 41, 11, 12, 13, 14, 15, 16, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 42]) total number of confs: 119 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517077 none CC1=C(C(=O)[O-])OC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 9, 9, 9, 23, 55, 55, 23, 28, 167, 167, 167, 167, 55, 55, 1, 2, 2, 2, 9, 23, 23, 55, 55, 167, 156, 167, 167, 167, 167, 140, 167, 55, 55, 1] 167 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 42, 23] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 403 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517077 none CC1=C(C(=O)[O-])OC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [167, 167, 167, 167, 167, 167, 167, 109, 109, 109, 17, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 167, 167, 167, 167, 109, 17, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 167] 167 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 40, 41, 42]) total number of confs: 378 number of broken/clashed sets: 8 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517077 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517077 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517077/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517077 Building REAL300004517078 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517078' /scratch/stefan/7774842/working/building/REAL300004517078 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517078 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517078/0 /scratch/stefan/7774842/working/building/REAL300004517078 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 107) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/107 `/scratch/stefan/7774842/working/3D/107' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN(CC(=O)NCC2=CC=C(N3CCCC3)C=C2)N=C1) `REAL300004517078.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517078.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517078/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517078 none O=C([O-])C1=CN(CC(=O)NCC2=CC=C(N3CCCC3)C=C2)N=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 99, 99, 99, 53, 20, 20, 20, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 99, 99, 99, 53, 53, 20, 4, 4, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 99] 201 rigid atoms, others: [40, 41, 10, 11, 12, 13, 14, 15, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 42]) total number of confs: 278 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517078 none O=C([O-])C1=CN(CC(=O)NCC2=CC=C(N3CCCC3)C=C2)N=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 7, 27, 27, 27, 65, 99, 99, 65, 82, 201, 201, 201, 201, 99, 99, 1, 1, 1, 7, 7, 27, 65, 65, 99, 99, 201, 200, 201, 201, 201, 201, 198, 201, 99, 99, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 42, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 597 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517078 none O=C([O-])C1=CN(CC(=O)NCC2=CC=C(N3CCCC3)C=C2)N=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 139, 58, 58, 58, 13, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201, 201, 139, 139, 58, 13, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 40, 41, 42]) total number of confs: 647 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517078 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517078 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517078/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517078 Building REAL300004517079 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517079' /scratch/stefan/7774842/working/building/REAL300004517079 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517079 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517079/0 /scratch/stefan/7774842/working/building/REAL300004517079 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 108) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/108 `/scratch/stefan/7774842/working/3D/108' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=CC1=CC=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)O1) `REAL300004517079.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517079.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517079/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517079 none O=C([O-])C=CC1=CC=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [114, 86, 114, 86, 36, 36, 36, 36, 23, 23, 23, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 36, 86, 86, 36, 36, 23, 4, 4, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1] 201 rigid atoms, others: [32, 33, 42, 43, 12, 13, 14, 15, 16, 17, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 335 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517079 none O=C([O-])C=CC1=CC=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 8, 24, 8, 1, 1, 1, 1, 1, 1, 3, 3, 3, 16, 36, 36, 16, 18, 121, 121, 121, 121, 36, 36, 1, 8, 8, 1, 1, 3, 16, 16, 36, 36, 121, 103, 121, 121, 121, 121, 107, 121, 36, 36] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 24, 27, 28] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 341 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517079 none O=C([O-])C=CC1=CC=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 121, 121, 121, 121, 89, 89, 89, 17, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 121, 201, 201, 121, 121, 89, 17, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 42, 43]) total number of confs: 580 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517079 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517079 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517079/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517079 Building REAL300004517080 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517080' /scratch/stefan/7774842/working/building/REAL300004517080 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517080 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517080/0 /scratch/stefan/7774842/working/building/REAL300004517080 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 109) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/109 `/scratch/stefan/7774842/working/3D/109' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1(C(=O)NCC2=CC=C(N3CCCC3)C=C2)CC2(CCC2)C1) `REAL300004517080.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517080.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517080/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517080 none O=C([O-])C1(C(=O)NCC2=CC=C(N3CCCC3)C=C2)CC2(CCC2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [112, 72, 112, 28, 28, 28, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 1, 72, 72, 72, 72, 72, 72, 28, 5, 5, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 72, 72, 72, 72, 72, 72, 72, 72, 72, 72] 201 rigid atoms, others: [38, 7, 8, 9, 10, 11, 12, 17, 18, 39, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 372 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517080 none O=C([O-])C1(C(=O)NCC2=CC=C(N3CCCC3)C=C2)CC2(CCC2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 5, 5, 5, 24, 72, 72, 36, 36, 201, 201, 201, 201, 72, 72, 1, 1, 1, 1, 1, 1, 5, 24, 24, 72, 72, 201, 201, 201, 201, 201, 201, 201, 201, 72, 72, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 3, 4, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 20, 21, 22, 23, 24] set([0, 2, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 430 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517080 none O=C([O-])C1(C(=O)NCC2=CC=C(N3CCCC3)C=C2)CC2(CCC2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 99, 99, 99, 18, 4, 4, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 201, 201, 201, 201, 201, 201, 99, 18, 18, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 603 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517080 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517080 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517080/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517080 Building REAL300004517081 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517081' /scratch/stefan/7774842/working/building/REAL300004517081 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517081 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517081/0 /scratch/stefan/7774842/working/building/REAL300004517081 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 110) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/110 `/scratch/stefan/7774842/working/3D/110' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C1) `REAL300004517081.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517081/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517081 none O=C([O-])COC1=CC=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [122, 106, 122, 74, 41, 28, 43, 43, 13, 13, 13, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 43, 43, 106, 106, 43, 43, 13, 3, 3, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 43, 43] 201 rigid atoms, others: [33, 34, 44, 43, 12, 13, 14, 15, 16, 17, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46]) total number of confs: 442 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517081 none O=C([O-])COC1=CC=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 9, 15, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 29, 43, 43, 29, 29, 95, 96, 96, 95, 43, 43, 1, 1, 9, 9, 1, 1, 5, 29, 29, 43, 43, 96, 95, 96, 96, 96, 96, 95, 96, 43, 43, 1, 1] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 45, 46, 24, 25, 28, 29] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 293 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517081 none O=C([O-])COC1=CC=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 146, 96, 63, 96, 96, 37, 37, 37, 13, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 96, 96, 201, 201, 96, 96, 37, 13, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 96, 96] 201 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 43, 44, 45, 46]) total number of confs: 742 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517081 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517081 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517081/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517081 Building REAL300004517082 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517082' /scratch/stefan/7774842/working/building/REAL300004517082 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517082 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517082/0 /scratch/stefan/7774842/working/building/REAL300004517082 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 111) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/111 `/scratch/stefan/7774842/working/3D/111' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=NN(C2=CC=CC=C2)C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C1) `REAL300004517082.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517082/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517082 none O=C([O-])C1=NN(C2=CC=CC=C2)C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [10, 4, 10, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 9, 9, 9, 30, 50, 50, 30, 30, 111, 134, 134, 111, 50, 50, 4, 1, 1, 1, 1, 1, 4, 9, 30, 30, 50, 50, 111, 111, 134, 134, 134, 134, 111, 111, 50, 50, 4, 4] 134 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 11, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 383 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517082 none O=C([O-])C1=NN(C2=CC=CC=C2)C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [134, 133, 134, 133, 133, 133, 133, 134, 134, 134, 134, 134, 86, 86, 86, 18, 4, 3, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 133, 134, 134, 134, 134, 134, 133, 86, 18, 18, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 133, 133] 134 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 48, 49, 50, 51]) total number of confs: 408 number of broken/clashed sets: 3 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517082 none O=C([O-])C1=NN(C2=CC=CC=C2)C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 1, 1, 1, 1, 4, 4, 4, 4, 4, 1, 1, 5, 5, 5, 20, 41, 41, 20, 20, 104, 133, 133, 104, 41, 41, 1, 4, 4, 4, 4, 4, 1, 5, 20, 20, 41, 41, 104, 104, 133, 133, 133, 133, 104, 104, 41, 41, 1, 1] 134 rigid atoms, others: [1, 34, 3, 4, 5, 6, 12, 13, 50, 51, 28] set([0, 2, 7, 8, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 353 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517082 none O=C([O-])C1=NN(C2=CC=CC=C2)C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [52, 41, 52, 41, 41, 41, 41, 50, 50, 50, 50, 50, 23, 23, 23, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 1, 41, 50, 50, 50, 50, 50, 41, 23, 4, 4, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 41, 41] 134 rigid atoms, others: [48, 49, 38, 39, 16, 17, 18, 19, 20, 21, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 50, 51]) total number of confs: 184 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517082 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517082 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517082/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517082 Building REAL300004517083 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517083' /scratch/stefan/7774842/working/building/REAL300004517083 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517083 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517083/0 /scratch/stefan/7774842/working/building/REAL300004517083 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 112) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/112 `/scratch/stefan/7774842/working/3D/112' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CSCCC(=O)NCC1=CC=C(N2CCCC2)C=C1) `REAL300004517083.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517083 none O=C([O-])CSCCC(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 14, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 192, 128, 126, 27, 27, 27, 9, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201, 128, 128, 126, 126, 27, 9, 9, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 41, 42]) total number of confs: 635 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517083 none O=C([O-])CSCCC(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 14, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [142, 138, 142, 114, 64, 62, 12, 12, 12, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 138, 138, 64, 64, 62, 62, 12, 4, 4, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1] 201 rigid atoms, others: [32, 41, 10, 11, 12, 13, 14, 15, 20, 21, 42, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 465 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517083 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517083 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517083/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517083 Building REAL300004517084 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517084' /scratch/stefan/7774842/working/building/REAL300004517084 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517084 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517084/0 /scratch/stefan/7774842/working/building/REAL300004517084 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 113) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/113 `/scratch/stefan/7774842/working/3D/113' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)N=C1) `REAL300004517084.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517084.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517084/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517084 none O=C([O-])C1=CC=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)N=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 8, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 32, 32, 32, 23, 23, 23, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 32, 32, 32, 32, 23, 5, 5, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 32] 78 rigid atoms, others: [39, 40, 10, 11, 12, 13, 14, 15, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 41]) total number of confs: 82 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517084 none O=C([O-])C1=CC=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)N=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 8, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 7, 7, 7, 19, 32, 32, 20, 25, 78, 78, 78, 78, 32, 32, 1, 1, 1, 1, 7, 19, 19, 32, 32, 78, 74, 78, 78, 78, 78, 73, 78, 32, 32, 1] 78 rigid atoms, others: [1, 3, 4, 5, 6, 7, 41, 22, 23, 24, 25] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 201 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517084 none O=C([O-])C1=CC=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)N=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 8, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [78, 78, 78, 78, 78, 78, 70, 70, 70, 17, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 78, 78, 78, 78, 70, 17, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 78] 78 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 39, 40, 41]) total number of confs: 212 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517084 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517084 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517084/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517084 Building REAL300004517085 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517085' /scratch/stefan/7774842/working/building/REAL300004517085 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517085 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517085/0 /scratch/stefan/7774842/working/building/REAL300004517085 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 114) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/114 `/scratch/stefan/7774842/working/3D/114' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C(C(=O)[O-])C=C1C(=O)NCC1=CC=C(N2CCCC2)C=C1) `REAL300004517085.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517085.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517085/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517085 none CN1N=C(C(=O)[O-])C=C1C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 38, 38, 38, 38, 38, 38, 22, 22, 22, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 1, 38, 38, 38, 38, 22, 5, 5, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1] 106 rigid atoms, others: [32, 41, 42, 12, 13, 14, 15, 16, 17, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 90 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517085 none CN1N=C(C(=O)[O-])C=C1C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 32, 38, 38, 32, 32, 89, 106, 106, 89, 38, 38, 2, 2, 2, 1, 10, 32, 32, 38, 38, 89, 92, 106, 106, 106, 106, 92, 89, 38, 38] 106 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 27] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 293 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517085 none CN1N=C(C(=O)[O-])C=C1C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 106, 106, 106, 106, 106, 106, 76, 76, 76, 18, 4, 4, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 106, 106, 106, 106, 76, 18, 18, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 106 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 41, 42]) total number of confs: 265 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517085 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517085 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517085/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517085 Building REAL300004517086 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517086' /scratch/stefan/7774842/working/building/REAL300004517086 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517086 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517086/0 /scratch/stefan/7774842/working/building/REAL300004517086 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 115) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/115 `/scratch/stefan/7774842/working/3D/115' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H](C(=O)NCC2=CC=C(N3CCCC3)C=C2)O[C@H]1C(=O)[O-]) `REAL300004517086.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517086.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517086/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517086 none C[C@@H]1C[C@H](C(=O)NCC2=CC=C(N3CCCC3)C=C2)O[C@H]1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 12, 5, 7, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 83, 83, 25, 83, 25, 25, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 83, 83, 83, 83, 115, 115, 83, 83, 83, 83, 83, 25, 4, 4, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1] 201 rigid atoms, others: [35, 36, 9, 10, 11, 12, 13, 14, 45, 19, 20, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 354 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517086 none C[C@@H]1C[C@H](C(=O)NCC2=CC=C(N3CCCC3)C=C2)O[C@H]1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 12, 5, 7, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 42, 83, 83, 42, 42, 189, 201, 201, 190, 83, 83, 1, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 8, 42, 42, 83, 83, 198, 190, 201, 201, 201, 201, 193, 200, 83, 83] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 579 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517086 none C[C@@H]1C[C@H](C(=O)NCC2=CC=C(N3CCCC3)C=C2)O[C@H]1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 12, 5, 7, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 89, 201, 89, 89, 17, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 89, 17, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 201 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 45, 46]) total number of confs: 586 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517086 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517086 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517086/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517086 Building REAL300004517087 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517087' /scratch/stefan/7774842/working/building/REAL300004517087 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517087 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517087/0 /scratch/stefan/7774842/working/building/REAL300004517087 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 116) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/116 `/scratch/stefan/7774842/working/3D/116' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CCC(=O)[O-])C(=O)NCC1=CC=C(N2CCCC2)C=C1) `REAL300004517087.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517087.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517087/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517087 none CC(C)(CCC(=O)[O-])C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 11, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [121, 74, 121, 121, 201, 201, 201, 201, 74, 74, 14, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 121, 121, 121, 121, 121, 121, 201, 201, 201, 201, 74, 14, 14, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 201 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 46, 47]) total number of confs: 959 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517087 none CC(C)(CCC(=O)[O-])C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 11, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 22, 39, 39, 69, 69, 100, 100, 22, 22, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 39, 39, 39, 39, 39, 39, 69, 69, 69, 69, 22, 5, 5, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1] 201 rigid atoms, others: [36, 37, 11, 12, 13, 14, 15, 16, 21, 22, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 465 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517087 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517087 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517087/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517087 Building REAL300004517088 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517088' /scratch/stefan/7774842/working/building/REAL300004517088 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517088 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517088/0 /scratch/stefan/7774842/working/building/REAL300004517088 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 117) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/117 `/scratch/stefan/7774842/working/3D/117' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C1) `REAL300004517088.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517088.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517088/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517088 none O=C([O-])CC1=CC=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [81, 75, 81, 75, 75, 75, 75, 27, 27, 27, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 1, 1, 75, 75, 75, 75, 75, 75, 27, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 75, 75] 179 rigid atoms, others: [32, 33, 43, 42, 11, 12, 13, 14, 15, 16, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45]) total number of confs: 169 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517088 none O=C([O-])CC1=CC=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 7, 7, 7, 32, 75, 75, 32, 45, 179, 179, 179, 179, 75, 75, 1, 1, 2, 2, 1, 1, 7, 32, 32, 75, 75, 179, 178, 179, 179, 179, 179, 167, 179, 75, 75, 1, 1] 179 rigid atoms, others: [3, 4, 5, 6, 7, 8, 44, 45, 23, 24, 27, 28] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 494 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517088 none O=C([O-])CC1=CC=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [179, 179, 179, 179, 179, 179, 179, 89, 89, 89, 23, 4, 3, 7, 7, 1, 1, 1, 1, 1, 1, 7, 7, 179, 179, 179, 179, 179, 179, 89, 23, 23, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 179, 179] 179 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 42, 43, 44, 45]) total number of confs: 400 number of broken/clashed sets: 15 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517088 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517088 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517088/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517088 Building REAL300004517089 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517089' /scratch/stefan/7774842/working/building/REAL300004517089 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517089 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517089/0 /scratch/stefan/7774842/working/building/REAL300004517089 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 118) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/118 `/scratch/stefan/7774842/working/3D/118' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=CC1=CC=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C1) `REAL300004517089.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517089.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517089/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517089 none O=C([O-])C=CC1=CC=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [108, 96, 108, 96, 75, 45, 77, 77, 24, 24, 24, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 77, 77, 96, 96, 77, 77, 24, 4, 4, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 77, 77] 201 rigid atoms, others: [33, 34, 44, 43, 12, 13, 14, 15, 16, 17, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46]) total number of confs: 420 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517089 none O=C([O-])C=CC1=CC=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [12, 4, 12, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 29, 77, 77, 29, 29, 165, 201, 201, 164, 77, 77, 1, 1, 4, 4, 1, 1, 5, 29, 29, 77, 77, 171, 171, 201, 201, 201, 201, 164, 182, 77, 77, 1, 1] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 45, 46, 24, 25, 28, 29] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 642 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517089 none O=C([O-])C=CC1=CC=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 134, 201, 201, 84, 84, 84, 17, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201, 201, 201, 201, 201, 84, 17, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201] 201 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 43, 44, 45, 46]) total number of confs: 735 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517089 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517089 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517089/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517089 Building REAL300004517090 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517090' /scratch/stefan/7774842/working/building/REAL300004517090 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517090 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517090/0 /scratch/stefan/7774842/working/building/REAL300004517090 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 119) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/119 `/scratch/stefan/7774842/working/3D/119' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=COC(C=CC(=O)NCC2=CC=C(N3CCCC3)C=C2)=C1) `REAL300004517090.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517090.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517090/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517090 none O=C([O-])C1=COC(C=CC(=O)NCC2=CC=C(N3CCCC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 12, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 105, 105, 105, 105, 73, 73, 19, 19, 19, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 105, 105, 73, 73, 19, 3, 3, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 105] 201 rigid atoms, others: [32, 41, 42, 12, 13, 14, 15, 16, 17, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 43]) total number of confs: 250 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517090 none O=C([O-])C1=COC(C=CC(=O)NCC2=CC=C(N3CCCC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 12, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 28, 28, 28, 86, 105, 105, 86, 86, 201, 201, 201, 201, 105, 105, 1, 1, 6, 6, 28, 86, 86, 105, 105, 201, 201, 201, 201, 201, 201, 201, 201, 105, 105, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 43, 24, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 534 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517090 none O=C([O-])C1=COC(C=CC(=O)NCC2=CC=C(N3CCCC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 12, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 155, 155, 63, 63, 63, 13, 4, 3, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201, 155, 155, 63, 13, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 201] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 41, 42, 43]) total number of confs: 537 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517090 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517090 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517090/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517090 Building REAL300004517091 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517091' /scratch/stefan/7774842/working/building/REAL300004517091 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517091 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517091/0 /scratch/stefan/7774842/working/building/REAL300004517091 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 120) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/120 `/scratch/stefan/7774842/working/3D/120' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CCC1=CC=CC=C1C(=O)NCC1=CC=C(N2CCCC2)C=C1) `REAL300004517091.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517091.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517091/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517091 none O=C([O-])CCC1=CC=CC=C1C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [51, 45, 51, 39, 27, 27, 27, 27, 27, 27, 13, 13, 13, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 45, 45, 39, 39, 27, 27, 27, 27, 13, 3, 3, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1] 127 rigid atoms, others: [48, 37, 38, 14, 15, 16, 17, 18, 19, 24, 25, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 188 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517091 none O=C([O-])CCC1=CC=CC=C1C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [13, 7, 12, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 19, 27, 27, 19, 21, 83, 83, 83, 83, 27, 27, 7, 7, 5, 5, 1, 1, 1, 1, 7, 19, 19, 27, 27, 83, 82, 83, 83, 83, 83, 82, 83, 27, 27] 127 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 10, 11, 30, 31] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 227 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517091 none O=C([O-])CCC1=CC=CC=C1C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [127, 127, 127, 113, 83, 83, 83, 83, 83, 83, 47, 47, 47, 13, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 127, 127, 113, 113, 83, 83, 83, 83, 47, 13, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 127 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 47, 48]) total number of confs: 450 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517091 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517091 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517091/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517091 Building REAL300004517092 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517092' /scratch/stefan/7774842/working/building/REAL300004517092 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517092 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517092/0 /scratch/stefan/7774842/working/building/REAL300004517092 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 121) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/121 `/scratch/stefan/7774842/working/3D/121' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(COCC(=O)NCC2=CC=C(N3CCCC3)C=C2)OC=N1) `REAL300004517092.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517092/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517092 none O=C([O-])C1=C(COCC(=O)NCC2=CC=C(N3CCCC3)C=C2)OC=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 5, 12, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [150, 150, 150, 150, 130, 54, 32, 11, 11, 11, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 150, 150, 150, 130, 130, 33, 33, 11, 3, 3, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 150] 201 rigid atoms, others: [33, 34, 43, 44, 11, 12, 13, 14, 15, 16, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 45]) total number of confs: 538 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517092 none O=C([O-])C1=C(COCC(=O)NCC2=CC=C(N3CCCC3)C=C2)OC=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 5, 12, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 21, 52, 78, 78, 78, 137, 150, 150, 137, 143, 201, 201, 201, 201, 150, 150, 1, 1, 1, 5, 5, 52, 52, 78, 137, 137, 150, 150, 201, 201, 201, 201, 201, 201, 201, 201, 150, 150, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 45, 23, 24, 25] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 696 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517092 none O=C([O-])C1=C(COCC(=O)NCC2=CC=C(N3CCCC3)C=C2)OC=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 5, 12, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 177, 85, 53, 23, 23, 23, 9, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201, 201, 177, 177, 54, 54, 23, 9, 9, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 201] 201 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 43, 44, 45]) total number of confs: 735 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517092 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517092 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517092/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517092 Building REAL300004517093 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517093' /scratch/stefan/7774842/working/building/REAL300004517093 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517093 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517093/0 /scratch/stefan/7774842/working/building/REAL300004517093 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 122) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/122 `/scratch/stefan/7774842/working/3D/122' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=CC(=O)NCC2=CC=C(N3CCCC3)C=C2)O1) `REAL300004517093.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517093/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517093 none O=C([O-])C1=CC=C(C=CC(=O)NCC2=CC=C(N3CCCC3)C=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 99, 99, 99, 99, 62, 62, 21, 21, 21, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 98, 99, 99, 62, 62, 21, 4, 4, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1] 201 rigid atoms, others: [32, 33, 42, 43, 12, 13, 14, 15, 16, 17, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 238 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517093 none O=C([O-])C1=CC=C(C=CC(=O)NCC2=CC=C(N3CCCC3)C=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 8, 34, 34, 34, 81, 99, 99, 81, 81, 196, 201, 201, 196, 99, 99, 1, 1, 1, 8, 8, 34, 81, 81, 99, 99, 197, 195, 201, 201, 201, 201, 195, 200, 99, 99] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 24, 25, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 567 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517093 none O=C([O-])C1=CC=C(C=CC(=O)NCC2=CC=C(N3CCCC3)C=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 161, 161, 74, 74, 74, 17, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201, 201, 161, 161, 74, 17, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 42, 43]) total number of confs: 534 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517093 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517093 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517093/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517093 Building REAL300004517094 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517094' /scratch/stefan/7774842/working/building/REAL300004517094 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517094 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517094/0 /scratch/stefan/7774842/working/building/REAL300004517094 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 123) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/123 `/scratch/stefan/7774842/working/3D/123' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])[C@@H]1CC[C@H](C(=O)NCC2=CC=C(N3CCCC3)C=C2)C1) `REAL300004517094.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517094 none O=C([O-])[C@@H]1CC[C@H](C(=O)NCC2=CC=C(N3CCCC3)C=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [93, 81, 93, 81, 81, 81, 81, 25, 81, 25, 25, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 81, 81, 81, 81, 81, 25, 4, 4, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 81, 81] 201 rigid atoms, others: [32, 33, 42, 43, 12, 13, 14, 15, 16, 17, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45]) total number of confs: 272 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517094 none O=C([O-])[C@@H]1CC[C@H](C(=O)NCC2=CC=C(N3CCCC3)C=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 37, 81, 81, 37, 42, 201, 201, 201, 201, 81, 81, 1, 1, 1, 1, 1, 9, 37, 37, 81, 81, 201, 183, 201, 201, 201, 201, 188, 201, 81, 81, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 44, 45, 24, 25, 26, 27, 28] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 519 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517094 none O=C([O-])[C@@H]1CC[C@H](C(=O)NCC2=CC=C(N3CCCC3)C=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 80, 201, 80, 80, 14, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201, 201, 201, 201, 80, 14, 14, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 42, 43, 44, 45]) total number of confs: 583 number of broken/clashed sets: 10 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517094 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517094 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517094/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517094 Building REAL300004517095 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517095' /scratch/stefan/7774842/working/building/REAL300004517095 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517095 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517095/0 /scratch/stefan/7774842/working/building/REAL300004517095 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 124) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/124 `/scratch/stefan/7774842/working/3D/124' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C1C(=O)[O-]) `REAL300004517095.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517095 none CC1=CC=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [62, 62, 62, 62, 24, 24, 24, 4, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 1, 1, 62, 62, 62, 71, 71, 62, 62, 62, 62, 62, 24, 4, 4, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 62] 201 rigid atoms, others: [33, 34, 43, 8, 9, 10, 11, 12, 13, 44, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 45]) total number of confs: 163 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517095 none CC1=CC=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 25, 62, 62, 25, 25, 183, 201, 201, 184, 62, 62, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 5, 25, 25, 62, 62, 201, 179, 201, 201, 201, 201, 181, 201, 62, 62, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 45, 20, 21, 22, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 544 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517095 none CC1=CC=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 96, 96, 96, 20, 4, 2, 7, 7, 1, 1, 1, 1, 1, 1, 7, 7, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 96, 20, 20, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 201] 201 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 43, 44, 45]) total number of confs: 437 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517095 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517095 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517095/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517095 Building REAL300004517096 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517096' /scratch/stefan/7774842/working/building/REAL300004517096 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517096 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517096/0 /scratch/stefan/7774842/working/building/REAL300004517096 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 125) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/125 `/scratch/stefan/7774842/working/3D/125' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN=CC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=C1) `REAL300004517096.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517096 none O=C([O-])C1=CN=CC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [44, 44, 44, 44, 44, 44, 44, 19, 19, 19, 5, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 44, 44, 44, 19, 5, 5, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 44] 127 rigid atoms, others: [39, 40, 11, 12, 13, 14, 15, 16, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 41]) total number of confs: 99 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517096 none O=C([O-])C1=CN=CC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 25, 44, 44, 25, 40, 127, 127, 127, 127, 44, 44, 1, 1, 1, 5, 25, 25, 44, 44, 127, 126, 127, 127, 127, 127, 116, 127, 44, 44, 1] 127 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 41, 23, 24, 25] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 338 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517096 none O=C([O-])C1=CN=CC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [127, 127, 127, 127, 127, 127, 127, 67, 67, 67, 23, 4, 3, 8, 8, 1, 1, 1, 1, 1, 1, 8, 8, 127, 127, 127, 67, 23, 23, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 127] 127 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 39, 40, 41]) total number of confs: 312 number of broken/clashed sets: 7 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517096 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517096 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517096/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517096 Building REAL300004517097 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517097' /scratch/stefan/7774842/working/building/REAL300004517097 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517097 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517097/0 /scratch/stefan/7774842/working/building/REAL300004517097 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 126) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/126 `/scratch/stefan/7774842/working/3D/126' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=C(C(=O)[O-])C=C1C(=O)NCC1=CC=C(N2CCCC2)C=C1) `REAL300004517097.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517097/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517097 none CC1=NC=C(C(=O)[O-])C=C1C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [87, 87, 87, 87, 87, 87, 87, 87, 87, 26, 26, 26, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 87, 87, 87, 87, 87, 26, 5, 5, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1] 201 rigid atoms, others: [33, 34, 43, 44, 13, 14, 15, 16, 17, 18, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 154 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517097 none CC1=NC=C(C(=O)[O-])C=C1C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 51, 87, 87, 51, 51, 187, 201, 201, 194, 87, 87, 2, 2, 2, 1, 1, 10, 51, 51, 87, 87, 201, 188, 201, 201, 201, 201, 195, 201, 87, 87] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 585 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517097 none CC1=NC=C(C(=O)[O-])C=C1C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 89, 89, 89, 17, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201, 201, 201, 201, 89, 17, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 201 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 43, 44]) total number of confs: 407 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517097 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517097 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517097/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517097 Building REAL300004517098 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517098' /scratch/stefan/7774842/working/building/REAL300004517098 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517098 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517098/0 /scratch/stefan/7774842/working/building/REAL300004517098 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 127) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/127 `/scratch/stefan/7774842/working/3D/127' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=NN(CC(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C1) `REAL300004517098.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517098.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517098/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517098 none O=C([O-])C1=NN(CC(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [89, 89, 89, 89, 89, 68, 21, 21, 21, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 89, 89, 68, 68, 21, 4, 4, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 89, 89] 201 rigid atoms, others: [39, 40, 10, 11, 12, 13, 14, 15, 20, 21, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42]) total number of confs: 300 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517098 none O=C([O-])C1=NN(CC(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 7, 19, 19, 19, 54, 89, 89, 54, 54, 188, 194, 193, 188, 89, 89, 1, 1, 7, 7, 19, 54, 54, 89, 89, 188, 188, 201, 201, 195, 201, 188, 188, 89, 89, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 41, 42, 22, 23] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 586 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517098 none O=C([O-])C1=NN(CC(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 166, 73, 73, 73, 14, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201, 166, 166, 73, 14, 14, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 39, 40, 41, 42]) total number of confs: 697 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517098 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517098 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517098/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517098 Building REAL300004517099 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517099' /scratch/stefan/7774842/working/building/REAL300004517099 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517099 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517099/0 /scratch/stefan/7774842/working/building/REAL300004517099 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 128) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/128 `/scratch/stefan/7774842/working/3D/128' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=NN(CCCC(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C1) `REAL300004517099.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517099.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517099/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517099 none O=C([O-])C1=NN(CCCC(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [112, 112, 112, 112, 112, 101, 91, 79, 21, 21, 21, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 112, 112, 98, 98, 97, 97, 79, 79, 21, 3, 3, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 112, 112] 201 rigid atoms, others: [45, 35, 36, 12, 13, 14, 15, 16, 17, 46, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48]) total number of confs: 462 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517099 none O=C([O-])C1=NN(CCCC(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 7, 11, 20, 36, 36, 36, 84, 112, 112, 84, 84, 201, 201, 201, 201, 112, 112, 1, 1, 7, 7, 11, 11, 20, 20, 36, 84, 84, 112, 112, 201, 201, 201, 201, 201, 201, 201, 201, 112, 112, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 47, 48, 24, 25] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 654 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517099 none O=C([O-])C1=NN(CCCC(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 192, 182, 166, 56, 56, 56, 13, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201, 188, 188, 190, 190, 166, 166, 56, 13, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201] 201 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 45, 46, 47, 48]) total number of confs: 797 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517099 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517099 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517099/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517099 Building REAL300004517100 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517100' /scratch/stefan/7774842/working/building/REAL300004517100 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517100 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517100/0 /scratch/stefan/7774842/working/building/REAL300004517100 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 129) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/129 `/scratch/stefan/7774842/working/3D/129' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])[C@@H]1CC[C@@H]1C(=O)NCC1=CC=C(N2CCCC2)C=C1) `REAL300004517100.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517100/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517100 none O=C([O-])[C@@H]1CC[C@@H]1C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [60, 52, 60, 52, 52, 52, 52, 25, 52, 25, 25, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 1, 52, 52, 52, 52, 25, 4, 4, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1] 110 rigid atoms, others: [32, 41, 42, 12, 13, 14, 15, 16, 17, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 185 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517100 none O=C([O-])[C@@H]1CC[C@@H]1C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 25, 52, 52, 25, 30, 110, 110, 110, 110, 52, 52, 1, 1, 1, 1, 6, 25, 25, 52, 52, 110, 103, 110, 110, 110, 110, 100, 110, 52, 52] 110 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 24, 25, 26, 27] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 324 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517100 none O=C([O-])[C@@H]1CC[C@@H]1C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [110, 110, 110, 110, 110, 110, 110, 74, 110, 74, 74, 18, 4, 4, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 110, 110, 110, 110, 74, 18, 18, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 110 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 41, 42]) total number of confs: 339 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517100 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517100 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517100/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517100 Building REAL300004517101 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517101' /scratch/stefan/7774842/working/building/REAL300004517101 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517101 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517101/0 /scratch/stefan/7774842/working/building/REAL300004517101 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 130) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/130 `/scratch/stefan/7774842/working/3D/130' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC[C@@H]1CC[C@H](C(=O)NCC2=CC=C(N3CCCC3)C=C2)O1) `REAL300004517101.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517101/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517101 none O=C([O-])CC[C@@H]1CC[C@H](C(=O)NCC2=CC=C(N3CCCC3)C=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [112, 101, 112, 90, 44, 44, 44, 44, 44, 20, 44, 20, 20, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 44, 101, 101, 90, 90, 44, 44, 44, 44, 20, 4, 4, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1] 201 rigid atoms, others: [48, 49, 38, 39, 14, 15, 16, 17, 18, 19, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 469 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517101 none O=C([O-])CC[C@@H]1CC[C@H](C(=O)NCC2=CC=C(N3CCCC3)C=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 11, 18, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 24, 44, 44, 24, 24, 116, 117, 117, 115, 44, 44, 1, 11, 11, 6, 6, 1, 1, 1, 1, 6, 24, 24, 44, 44, 117, 116, 117, 117, 117, 117, 114, 117, 44, 44] 201 rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 10, 11, 26, 31] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 362 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517101 none O=C([O-])CC[C@@H]1CC[C@H](C(=O)NCC2=CC=C(N3CCCC3)C=C2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 187, 117, 117, 117, 117, 117, 64, 117, 64, 64, 14, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 117, 201, 201, 187, 187, 117, 117, 117, 117, 64, 14, 14, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 201 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 48, 49]) total number of confs: 811 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517101 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517101 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517101/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517101 Building REAL300004517102 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517102' /scratch/stefan/7774842/working/building/REAL300004517102 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517102 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517102/0 /scratch/stefan/7774842/working/building/REAL300004517102 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 131) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/131 `/scratch/stefan/7774842/working/3D/131' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(CC[C@@H]1C[C@H](C(=O)[O-])CO1)NCC1=CC=C(N2CCCC2)C=C1) `REAL300004517102.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517102.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517102/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517102 none O=C(CC[C@@H]1C[C@H](C(=O)[O-])CO1)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 7, 5, 5, 7, 1, 11, 11, 5, 12, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1] 5 rigid atoms, others: [48, 49, 38, 39, 15, 16, 17, 18, 19, 20, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 12 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517102 none O=C(CC[C@@H]1C[C@H](C(=O)[O-])CO1)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 7, 5, 5, 7, 1, 11, 11, 5, 12, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 2, 2, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 2, 2, 2, 2, 2, 2, 2, 5, 5, 5, 5, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 2, 2] 5 rigid atoms, others: [32, 33, 34, 3, 4, 5, 6, 7, 8, 9, 12, 13, 31] set([0, 1, 2, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 15 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517102 none O=C(CC[C@@H]1C[C@H](C(=O)[O-])CO1)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'O.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 5, 5, 5, 7, 5, 5, 7, 1, 11, 11, 5, 12, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 5 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 48, 49]) total number of confs: 15 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517102 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517102 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517102/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517102 Building REAL300004517103 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517103' /scratch/stefan/7774842/working/building/REAL300004517103 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517103 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517103/0 /scratch/stefan/7774842/working/building/REAL300004517103 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 132) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/132 `/scratch/stefan/7774842/working/3D/132' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])[C@@H]1CC[C@@H]1C(=O)NCC1=CC=C(N2CCCC2)C=C1) `REAL300004517103.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517103 none O=C([O-])[C@@H]1CC[C@@H]1C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [60, 52, 60, 52, 52, 52, 52, 25, 52, 25, 25, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 1, 52, 52, 52, 52, 25, 4, 4, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1] 110 rigid atoms, others: [32, 41, 42, 12, 13, 14, 15, 16, 17, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 185 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517103 none O=C([O-])[C@@H]1CC[C@@H]1C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 25, 52, 52, 25, 30, 110, 110, 110, 110, 52, 52, 1, 1, 1, 1, 6, 25, 25, 52, 52, 110, 103, 110, 110, 110, 110, 100, 110, 52, 52] 110 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 24, 25, 26, 27] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 324 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517103 none O=C([O-])[C@@H]1CC[C@@H]1C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [110, 110, 110, 110, 110, 110, 110, 74, 110, 74, 74, 18, 4, 4, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 110, 110, 110, 110, 74, 18, 18, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 110 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 41, 42]) total number of confs: 339 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517103 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517103 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517103/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517103 Building REAL300004517104 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517104' /scratch/stefan/7774842/working/building/REAL300004517104 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517104 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517104/0 /scratch/stefan/7774842/working/building/REAL300004517104 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 133) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/133 `/scratch/stefan/7774842/working/3D/133' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)OC(C(=O)[O-])=C1) `REAL300004517104.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517104/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517104 none CC1=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)OC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 12, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [85, 85, 28, 28, 28, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 1, 85, 85, 85, 85, 85, 85, 85, 85, 85, 28, 5, 5, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 85] 165 rigid atoms, others: [6, 7, 8, 9, 10, 11, 16, 17, 41, 40, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 42]) total number of confs: 154 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517104 none CC1=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)OC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 12, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 9, 9, 9, 50, 85, 85, 51, 68, 165, 165, 165, 165, 85, 85, 1, 1, 1, 2, 2, 1, 2, 2, 2, 9, 50, 50, 85, 85, 165, 165, 165, 165, 165, 165, 161, 165, 85, 85, 1] 165 rigid atoms, others: [0, 1, 2, 3, 42, 18, 19, 20, 23] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 503 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517104 none CC1=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)OC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 12, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [165, 165, 96, 96, 96, 18, 4, 4, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 165, 165, 165, 165, 165, 165, 165, 165, 165, 96, 18, 18, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 165] 165 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 40, 41, 42]) total number of confs: 375 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517104 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517104 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517104/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517104 Building REAL300004517105 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517105' /scratch/stefan/7774842/working/building/REAL300004517105 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517105 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517105/0 /scratch/stefan/7774842/working/building/REAL300004517105 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 134) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/134 `/scratch/stefan/7774842/working/3D/134' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])[C@H]1C2C=CC(CC2)[C@H]1C(=O)NCC1=CC=C(N2CCCC2)C=C1) `REAL300004517105.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517105.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517105/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517105 none O=C([O-])[C@H]1C2C=CC(CC2)[C@H]1C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 1, 1, 5, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 13, 15, 13, 13, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 13, 5, 5, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1] 30 rigid atoms, others: [49, 39, 40, 50, 16, 17, 18, 19, 20, 21, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 51 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517105 none O=C([O-])[C@H]1C2C=CC(CC2)[C@H]1C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 1, 1, 5, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 10, 15, 15, 13, 13, 30, 30, 30, 30, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 3, 10, 10, 15, 15, 30, 30, 30, 30, 30, 30, 30, 30, 15, 15] 30 rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 35, 33, 28, 29, 30, 31] set([0, 2, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 77 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517105 none O=C([O-])[C@H]1C2C=CC(CC2)[C@H]1C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 1, 1, 5, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 28, 30, 28, 28, 13, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 30, 30, 30, 30, 30, 30, 30, 30, 28, 13, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 30 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 49, 50]) total number of confs: 95 number of broken/clashed sets: 8 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517105 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517105 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517105/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517105 Building REAL300004517106 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517106' /scratch/stefan/7774842/working/building/REAL300004517106 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517106 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517106/0 /scratch/stefan/7774842/working/building/REAL300004517106 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 135) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/135 `/scratch/stefan/7774842/working/3D/135' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(C(=O)[O-])C(=O)NCC1=CC=C(N2CCCC2)C=C1) `REAL300004517106.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517106 none CC(C)C(C(=O)[O-])C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [170, 155, 171, 85, 155, 158, 158, 85, 85, 17, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 171, 171, 171, 171, 171, 171, 171, 155, 85, 17, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 171 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 43, 44]) total number of confs: 709 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517106 none CC(C)C(C(=O)[O-])C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [83, 69, 85, 24, 69, 75, 75, 24, 24, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 85, 85, 85, 85, 85, 85, 85, 69, 24, 5, 5, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1] 171 rigid atoms, others: [33, 34, 43, 44, 10, 11, 12, 13, 14, 15, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 382 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517106 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517106 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517106/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517106 Building REAL300004517107 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517107' /scratch/stefan/7774842/working/building/REAL300004517107 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517107 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517107/0 /scratch/stefan/7774842/working/building/REAL300004517107 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 136) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/136 `/scratch/stefan/7774842/working/3D/136' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])[C@@H]1CCCC[C@@H]1C(=O)NCC1=CC=C(N2CCCC2)C=C1) `REAL300004517107.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517107 none O=C([O-])[C@@H]1CCCC[C@@H]1C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 32, 32, 26, 32, 26, 26, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 32, 32, 32, 32, 32, 32, 32, 32, 26, 5, 5, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1] 63 rigid atoms, others: [48, 37, 38, 14, 15, 16, 17, 18, 19, 24, 25, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 95 number of broken/clashed sets: 17 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517107 none O=C([O-])[C@@H]1CCCC[C@@H]1C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 13, 32, 32, 17, 32, 63, 63, 63, 63, 32, 32, 1, 1, 1, 1, 1, 1, 1, 1, 4, 13, 13, 32, 32, 63, 63, 63, 63, 63, 63, 63, 63, 32, 32] 63 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 33, 26, 27, 28, 29, 30, 31] set([0, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 179 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517107 none O=C([O-])[C@@H]1CCCC[C@@H]1C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 63, 63, 63, 63, 63, 63, 58, 63, 58, 58, 15, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 63, 63, 63, 63, 63, 63, 63, 63, 58, 15, 15, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 63 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 47, 48]) total number of confs: 182 number of broken/clashed sets: 17 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517107 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517107 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517107/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517107 Building REAL300004517108 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517108' /scratch/stefan/7774842/working/building/REAL300004517108 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300004517108 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517108/0 /scratch/stefan/7774842/working/building/REAL300004517108 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 137) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/137 `/scratch/stefan/7774842/working/3D/137' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1CCC[N@H+](CC(=O)NCC2=CC=C(N3CCCC3)C=C2)C1) `REAL300004517108.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517108/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517108 none O=C([O-])C1CCC[N@H+](CC(=O)NCC2=CC=C(N3CCCC3)C=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [35, 32, 35, 32, 32, 32, 32, 27, 32, 11, 11, 11, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 1, 1, 32, 32, 32, 32, 32, 32, 32, 32, 27, 27, 11, 3, 3, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 32, 32] 98 rigid atoms, others: [48, 49, 38, 39, 13, 14, 15, 16, 17, 18, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 50, 51]) total number of confs: 146 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517108 none O=C([O-])C1CCC[N@H+](CC(=O)NCC2=CC=C(N3CCCC3)C=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 4, 14, 14, 14, 23, 32, 32, 23, 23, 98, 98, 98, 94, 32, 32, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 14, 23, 23, 32, 32, 98, 98, 98, 98, 98, 98, 94, 98, 32, 32, 1, 1] 98 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 50, 51, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 241 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517108 none O=C([O-])C1CCC[N@H+](CC(=O)NCC2=CC=C(N3CCCC3)C=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 98 conformations in input total number of sets (complete confs): 98 using faster count positions algorithm for large data unique positions, atoms: [98, 98, 98, 98, 98, 98, 98, 93, 98, 42, 42, 42, 16, 4, 2, 7, 7, 1, 1, 1, 1, 1, 1, 7, 7, 98, 98, 98, 98, 98, 98, 98, 98, 93, 93, 42, 16, 16, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 98, 98] 98 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 48, 49, 50, 51]) total number of confs: 402 number of broken/clashed sets: 5 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517108 /scratch/stefan/7774842/working /scratch/stefan/7774842 mkdir: created directory `1' /scratch/stefan/7774842/working/building/REAL300004517108/1 /scratch/stefan/7774842/working/building/REAL300004517108 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 1 (index: 138) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/138 `/scratch/stefan/7774842/working/3D/138' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1CCC[N@@H+](CC(=O)NCC2=CC=C(N3CCCC3)C=C2)C1) `REAL300004517108.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004517108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517108/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517108 none O=C([O-])C1CCC[N@@H+](CC(=O)NCC2=CC=C(N3CCCC3)C=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [79, 79, 79, 79, 79, 79, 79, 65, 79, 19, 19, 19, 4, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 1, 1, 79, 79, 79, 79, 79, 79, 79, 79, 65, 65, 19, 4, 4, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 79, 79] 201 rigid atoms, others: [48, 49, 38, 39, 13, 14, 15, 16, 17, 18, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 50, 51]) total number of confs: 301 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517108 none O=C([O-])C1CCC[N@@H+](CC(=O)NCC2=CC=C(N3CCCC3)C=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 9, 24, 24, 24, 56, 79, 79, 79, 79, 201, 201, 201, 201, 79, 79, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 24, 56, 56, 79, 79, 201, 201, 201, 201, 201, 201, 201, 201, 79, 79, 1, 1] 201 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 50, 51, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 439 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517108 none O=C([O-])C1CCC[N@@H+](CC(=O)NCC2=CC=C(N3CCCC3)C=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 180, 201, 65, 65, 65, 15, 7, 6, 7, 7, 1, 1, 1, 1, 1, 1, 7, 7, 201, 201, 201, 201, 201, 201, 201, 201, 180, 180, 65, 15, 15, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 201, 201] 201 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 48, 49, 50, 51]) total number of confs: 731 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517108 /scratch/stefan/7774842/working /scratch/stefan/7774842 mkdir: created directory `2' /scratch/stefan/7774842/working/building/REAL300004517108/2 /scratch/stefan/7774842/working/building/REAL300004517108 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 2 (index: 139) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/139 `/scratch/stefan/7774842/working/3D/139' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1CCCN(CC(=O)NCC2=CC=C(N3CCCC3)C=C2)C1) `REAL300004517108.mol2' -> `2.mol2' `temp.mol2' -> `REAL300004517108.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517108/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517108 none O=C([O-])C1CCCN(CC(=O)NCC2=CC=C(N3CCCC3)C=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 74, 90, 74, 74, 74, 74, 62, 17, 17, 17, 4, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 1, 1, 74, 74, 74, 74, 74, 74, 74, 74, 62, 62, 17, 4, 4, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 74, 74] 201 rigid atoms, others: [48, 37, 38, 12, 13, 14, 15, 16, 17, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 49, 50]) total number of confs: 307 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517108 none O=C([O-])C1CCCN(CC(=O)NCC2=CC=C(N3CCCC3)C=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 7, 18, 18, 18, 44, 74, 74, 44, 58, 201, 201, 201, 201, 74, 74, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 18, 44, 44, 74, 74, 201, 197, 201, 201, 201, 201, 192, 201, 74, 74, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 49, 50, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 530 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517108 none O=C([O-])C1CCCN(CC(=O)NCC2=CC=C(N3CCCC3)C=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 10, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 181, 65, 65, 65, 18, 4, 3, 7, 7, 1, 1, 1, 1, 1, 1, 7, 7, 201, 201, 201, 201, 201, 201, 201, 201, 181, 181, 65, 18, 18, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 201, 201] 201 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 47, 48, 49, 50]) total number of confs: 718 number of broken/clashed sets: 10 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517108 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517108 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 2: /scratch/stefan/7774842/working/building/REAL300004517108/2.* 1: /scratch/stefan/7774842/working/building/REAL300004517108/1.* 0: /scratch/stefan/7774842/working/building/REAL300004517108/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517108 Building REAL300004517109 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517109' /scratch/stefan/7774842/working/building/REAL300004517109 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517109 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517109/0 /scratch/stefan/7774842/working/building/REAL300004517109 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 140) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/140 `/scratch/stefan/7774842/working/3D/140' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1(C(=O)NCC2=CC=C(N3CCCC3)C=C2)CC1C1=CC=CC=C1) `REAL300004517109.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517109/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517109 none O=C([O-])C1(C(=O)NCC2=CC=C(N3CCCC3)C=C2)CC1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [88, 88, 88, 27, 27, 27, 4, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 1, 1, 88, 88, 88, 88, 88, 88, 88, 88, 27, 4, 4, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 88, 88, 88, 88, 88, 88, 88, 88] 163 rigid atoms, others: [7, 8, 9, 10, 11, 12, 17, 18, 41, 40, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 246 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517109 none O=C([O-])C1(C(=O)NCC2=CC=C(N3CCCC3)C=C2)CC1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [2, 2, 2, 2, 2, 6, 6, 6, 32, 88, 88, 32, 32, 145, 163, 163, 148, 88, 88, 2, 1, 1, 1, 1, 1, 1, 1, 6, 32, 32, 88, 88, 155, 149, 163, 163, 163, 163, 148, 163, 88, 88, 2, 2, 2, 1, 1, 1, 1, 1] 163 rigid atoms, others: [45, 46, 47, 48, 49, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 556 number of broken/clashed sets: 11 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517109 none O=C([O-])C1(C(=O)NCC2=CC=C(N3CCCC3)C=C2)CC1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 6, 6, 6, 32, 88, 88, 32, 32, 146, 163, 163, 144, 88, 88, 1, 1, 1, 2, 2, 2, 2, 2, 6, 32, 32, 88, 88, 155, 151, 163, 163, 163, 163, 145, 162, 88, 88, 1, 1, 1, 2, 2, 2, 2, 2] 163 rigid atoms, others: [1, 3, 4, 42, 43, 44, 19, 20, 21] set([0, 2, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 45, 46, 47, 48, 49]) total number of confs: 580 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517109 none O=C([O-])C1(C(=O)NCC2=CC=C(N3CCCC3)C=C2)CC1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [163, 163, 163, 99, 99, 99, 20, 4, 2, 7, 7, 1, 1, 1, 1, 1, 1, 7, 7, 163, 163, 163, 163, 163, 163, 163, 163, 99, 20, 20, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 163, 163, 163, 163, 163, 163, 163, 163] 163 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 493 number of broken/clashed sets: 11 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517109 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517109 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517109/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517109 Building REAL300004517110 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517110' /scratch/stefan/7774842/working/building/REAL300004517110 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517110 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517110/0 /scratch/stefan/7774842/working/building/REAL300004517110 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 141) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/141 `/scratch/stefan/7774842/working/3D/141' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)NC2=CC=CC=C21) `REAL300004517110.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517110 none O=C([O-])CC1=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)NC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [55, 50, 55, 50, 50, 21, 21, 21, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 4, 4, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 50, 50, 50, 50, 50] 142 rigid atoms, others: [33, 34, 43, 9, 10, 11, 12, 13, 14, 44, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49]) total number of confs: 125 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517110 none O=C([O-])CC1=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)NC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [7, 2, 7, 1, 1, 1, 1, 7, 7, 7, 23, 50, 50, 23, 23, 109, 142, 142, 109, 50, 50, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 23, 23, 50, 50, 110, 109, 142, 142, 142, 142, 109, 114, 50, 50, 1, 1, 1, 1, 1] 142 rigid atoms, others: [3, 4, 5, 6, 45, 46, 47, 48, 49, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 407 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517110 none O=C([O-])CC1=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)NC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [142, 142, 142, 142, 142, 73, 73, 73, 17, 4, 3, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 142, 142, 142, 142, 142, 142, 142, 142, 142, 73, 17, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 142, 142, 142, 142, 142] 142 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 319 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517110 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517110 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517110/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517110 Building REAL300004517111 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517111' /scratch/stefan/7774842/working/building/REAL300004517111 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517111 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517111/0 /scratch/stefan/7774842/working/building/REAL300004517111 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 142) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/142 `/scratch/stefan/7774842/working/3D/142' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN(CC(=O)NCC2=CC=C(N3CCCC3)C=C2)C2=CC=CC=C12) `REAL300004517111.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517111.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517111/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517111 none O=C([O-])C1=CN(CC(=O)NCC2=CC=C(N3CCCC3)C=C2)C2=CC=CC=C12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [96, 96, 96, 96, 96, 64, 17, 17, 17, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 96, 96, 96, 96, 96, 96, 96, 64, 64, 17, 3, 3, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 96, 96, 96, 96] 201 rigid atoms, others: [34, 35, 44, 10, 11, 12, 13, 14, 15, 20, 21, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48, 49]) total number of confs: 296 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517111 none O=C([O-])C1=CN(CC(=O)NCC2=CC=C(N3CCCC3)C=C2)C2=CC=CC=C12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 7, 17, 17, 17, 71, 96, 96, 71, 76, 201, 201, 201, 201, 96, 96, 1, 1, 1, 1, 1, 1, 1, 7, 7, 17, 71, 71, 96, 96, 201, 197, 201, 201, 201, 201, 197, 201, 96, 96, 1, 1, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 46, 47, 48, 49, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 570 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517111 none O=C([O-])C1=CN(CC(=O)NCC2=CC=C(N3CCCC3)C=C2)C2=CC=CC=C12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 157, 57, 57, 57, 13, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201, 201, 201, 201, 201, 201, 157, 157, 57, 13, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201, 201, 201] 201 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 44, 45, 46, 47, 48, 49]) total number of confs: 667 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517111 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517111 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517111/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517111 Building REAL300004517112 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517112' /scratch/stefan/7774842/working/building/REAL300004517112 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517112 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517112/0 /scratch/stefan/7774842/working/building/REAL300004517112 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 143) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/143 `/scratch/stefan/7774842/working/3D/143' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1CC12CC(C(=O)NCC1=CC=C(N3CCCC3)C=C1)C2) `REAL300004517112.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517112.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517112/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517112 none O=C([O-])C1CC12CC(C(=O)NCC1=CC=C(N3CCCC3)C=C1)C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [88, 78, 88, 78, 78, 78, 78, 21, 21, 21, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 78, 78, 78, 78, 78, 78, 78, 21, 4, 4, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 78, 78] 201 rigid atoms, others: [33, 34, 43, 44, 11, 12, 13, 14, 15, 16, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46]) total number of confs: 250 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517112 none O=C([O-])C1CC12CC(C(=O)NCC1=CC=C(N3CCCC3)C=C1)C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 10, 10, 10, 45, 78, 78, 45, 48, 197, 201, 201, 199, 78, 78, 1, 1, 1, 1, 1, 1, 1, 10, 45, 45, 78, 78, 201, 194, 201, 201, 201, 201, 195, 201, 78, 78, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 45, 46, 23, 24, 25, 26, 27, 28, 29] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 519 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517112 none O=C([O-])C1CC12CC(C(=O)NCC1=CC=C(N3CCCC3)C=C1)C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 72, 72, 72, 14, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201, 201, 201, 201, 201, 201, 72, 14, 14, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201] 201 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 43, 44, 45, 46]) total number of confs: 551 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517112 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517112 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517112/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517112 Building REAL300004517113 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517113' /scratch/stefan/7774842/working/building/REAL300004517113 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517113 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517113/0 /scratch/stefan/7774842/working/building/REAL300004517113 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 144) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/144 `/scratch/stefan/7774842/working/3D/144' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])[C@H]1C[C@@H](C(=O)NCC2=CC=C(N3CCCC3)C=C2)C1) `REAL300004517113.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517113 none O=C([O-])[C@H]1C[C@@H](C(=O)NCC2=CC=C(N3CCCC3)C=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [93, 81, 93, 81, 81, 81, 25, 81, 25, 25, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 81, 81, 81, 25, 4, 4, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 81, 81] 201 rigid atoms, others: [39, 40, 11, 12, 13, 14, 15, 16, 21, 22, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42]) total number of confs: 262 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517113 none O=C([O-])[C@H]1C[C@@H](C(=O)NCC2=CC=C(N3CCCC3)C=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 13, 13, 13, 43, 81, 81, 43, 44, 197, 201, 201, 193, 81, 81, 1, 1, 1, 13, 43, 43, 81, 81, 201, 188, 201, 201, 201, 201, 190, 201, 81, 81, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 41, 42, 23, 24, 25] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 534 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517113 none O=C([O-])[C@H]1C[C@@H](C(=O)NCC2=CC=C(N3CCCC3)C=C2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 83, 201, 83, 83, 17, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201, 201, 83, 17, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 39, 40, 41, 42]) total number of confs: 572 number of broken/clashed sets: 16 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517113 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517113 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517113/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517113 Building REAL300004517114 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517114' /scratch/stefan/7774842/working/building/REAL300004517114 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517114 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517114/0 /scratch/stefan/7774842/working/building/REAL300004517114 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 145) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/145 `/scratch/stefan/7774842/working/3D/145' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@]1(C(=O)[O-])C[C@@H]1C(=O)NCC1=CC=C(N2CCCC2)C=C1) `REAL300004517114.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517114.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517114/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517114 none CC(C)[C@@]1(C(=O)[O-])C[C@@H]1C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [22, 21, 22, 21, 21, 21, 21, 21, 14, 21, 14, 14, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 22, 22, 22, 22, 22, 22, 22, 21, 21, 14, 4, 4, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1] 48 rigid atoms, others: [48, 37, 38, 13, 14, 15, 16, 17, 18, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 76 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517114 none CC(C)[C@@]1(C(=O)[O-])C[C@@H]1C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 2, 2, 1, 1, 1, 1, 4, 4, 4, 16, 21, 21, 21, 21, 48, 48, 48, 48, 21, 21, 3, 3, 3, 3, 3, 3, 3, 1, 1, 4, 16, 16, 21, 21, 48, 48, 48, 48, 48, 48, 48, 48, 21, 21] 48 rigid atoms, others: [32, 1, 3, 4, 33, 7, 8, 9, 10] set([0, 2, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517114 none CC(C)[C@@]1(C(=O)[O-])C[C@@H]1C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 48, 48, 48, 40, 48, 40, 40, 12, 5, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 48, 48, 48, 48, 48, 48, 48, 48, 48, 40, 12, 12, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 48 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 47, 48]) total number of confs: 148 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517114 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517114 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517114/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517114 Building REAL300004517115 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517115' /scratch/stefan/7774842/working/building/REAL300004517115 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517115 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517115/0 /scratch/stefan/7774842/working/building/REAL300004517115 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 146) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/146 `/scratch/stefan/7774842/working/3D/146' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)[O-])C=C1C(=O)NCC1=CC=C(N2CCCC2)C=C1) `REAL300004517115.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517115/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517115 none CC1=CC=C(C(=O)[O-])C=C1C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 106, 106, 106, 106, 106, 106, 106, 26, 26, 26, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 106, 106, 106, 106, 106, 106, 26, 5, 5, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1] 201 rigid atoms, others: [34, 35, 45, 44, 13, 14, 15, 16, 17, 18, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 175 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517115 none CC1=CC=C(C(=O)[O-])C=C1C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 10, 10, 10, 52, 106, 106, 52, 69, 201, 201, 201, 201, 106, 106, 2, 2, 2, 1, 1, 1, 10, 52, 52, 106, 106, 201, 198, 201, 201, 201, 201, 195, 201, 106, 106] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 8, 9, 10, 28, 29, 30] set([6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 621 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517115 none CC1=CC=C(C(=O)[O-])C=C1C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 89, 89, 89, 17, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201, 201, 201, 201, 201, 89, 17, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 201 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 44, 45]) total number of confs: 411 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517115 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517115 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517115/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517115 Building REAL300004517116 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517116' /scratch/stefan/7774842/working/building/REAL300004517116 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517116 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517116/0 /scratch/stefan/7774842/working/building/REAL300004517116 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 147) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/147 `/scratch/stefan/7774842/working/3D/147' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C(=O)[O-])CC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C1) `REAL300004517116.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517116/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517116 none CC1(C(=O)[O-])CC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 11, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 83, 83, 73, 22, 22, 22, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 73, 73, 73, 73, 73, 73, 73, 22, 4, 4, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 73, 73] 201 rigid atoms, others: [32, 33, 43, 10, 11, 12, 13, 14, 15, 20, 21, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45]) total number of confs: 240 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517116 none CC1(C(=O)[O-])CC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 11, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 1, 1, 1, 7, 7, 7, 29, 73, 73, 29, 50, 201, 201, 201, 201, 73, 73, 1, 2, 2, 2, 1, 1, 1, 7, 29, 29, 73, 73, 201, 196, 201, 201, 201, 201, 187, 201, 73, 73, 1, 1] 201 rigid atoms, others: [0, 1, 2, 5, 6, 7, 44, 45, 22, 26, 27, 28] set([3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 523 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517116 none CC1(C(=O)[O-])CC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 11, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 67, 67, 67, 13, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201, 201, 201, 201, 201, 201, 67, 13, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 42, 43, 44, 45]) total number of confs: 564 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517116 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517116 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517116/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517116 Building REAL300004517117 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517117' /scratch/stefan/7774842/working/building/REAL300004517117 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517117 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517117/0 /scratch/stefan/7774842/working/building/REAL300004517117 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 148) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/148 `/scratch/stefan/7774842/working/3D/148' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C=CS1) `REAL300004517117.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517117 none O=C([O-])C1=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [71, 67, 71, 67, 27, 27, 27, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 67, 67, 67, 27, 5, 5, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 67, 67] 163 rigid atoms, others: [36, 37, 8, 9, 10, 11, 12, 13, 18, 19, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39]) total number of confs: 145 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517117 none O=C([O-])C1=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 6, 6, 6, 33, 67, 67, 33, 36, 163, 163, 163, 163, 67, 67, 1, 1, 1, 6, 33, 33, 67, 67, 163, 146, 163, 163, 163, 163, 147, 163, 67, 67, 1, 1] 163 rigid atoms, others: [1, 3, 4, 5, 38, 39, 20, 21, 22] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 453 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517117 none O=C([O-])C1=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [163, 163, 163, 163, 75, 75, 75, 17, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 163, 163, 163, 75, 17, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 163, 163] 163 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 36, 37, 38, 39]) total number of confs: 342 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517117 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517117 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517117/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517117 Building REAL300004517118 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517118' /scratch/stefan/7774842/working/building/REAL300004517118 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517118 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517118/0 /scratch/stefan/7774842/working/building/REAL300004517118 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 149) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/149 `/scratch/stefan/7774842/working/3D/149' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=NNC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=C1) `REAL300004517118.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517118.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517118/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517118 none O=C([O-])C1=NNC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 35, 35, 35, 35, 22, 22, 22, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 35, 35, 22, 5, 5, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 35] 107 rigid atoms, others: [37, 38, 10, 11, 12, 13, 14, 15, 20, 21, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 39]) total number of confs: 87 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517118 none O=C([O-])C1=NNC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 25, 35, 35, 25, 33, 107, 107, 107, 107, 35, 35, 1, 1, 9, 25, 25, 35, 35, 107, 102, 107, 107, 107, 107, 96, 107, 35, 35, 1] 107 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 39, 22, 23] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 264 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517118 none O=C([O-])C1=NNC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 107, 107, 107, 81, 81, 81, 17, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 107, 107, 81, 17, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 107] 107 rigid atoms, others: [32, 33, 34, 35, 36, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 37, 38, 39]) total number of confs: 272 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517118 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517118 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517118/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517118 Building REAL300004517119 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517119' /scratch/stefan/7774842/working/building/REAL300004517119 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517119 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517119/0 /scratch/stefan/7774842/working/building/REAL300004517119 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 150) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/150 `/scratch/stefan/7774842/working/3D/150' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=NC=C1C(=O)NCC1=CC=C(N2CCCC2)C=C1) `REAL300004517119.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517119/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517119 none CC1=C(C(=O)[O-])C=NC=C1C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 8, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 103, 103, 103, 103, 103, 103, 103, 25, 25, 25, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 1, 103, 103, 103, 103, 103, 25, 4, 4, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1] 201 rigid atoms, others: [33, 34, 43, 44, 13, 14, 15, 16, 17, 18, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 172 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517119 none CC1=C(C(=O)[O-])C=NC=C1C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 8, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 10, 10, 10, 52, 103, 103, 52, 56, 201, 201, 201, 201, 103, 103, 2, 2, 2, 1, 1, 10, 52, 52, 103, 103, 201, 191, 201, 201, 201, 201, 193, 201, 103, 103] 201 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 9, 10, 28, 29] set([4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 612 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517119 none CC1=C(C(=O)[O-])C=NC=C1C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 8, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 94, 94, 94, 18, 4, 3, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 201, 201, 201, 201, 201, 94, 18, 18, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 201 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 43, 44]) total number of confs: 431 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517119 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517119 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517119/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517119 Building REAL300004517120 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517120' /scratch/stefan/7774842/working/building/REAL300004517120 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517120 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517120/0 /scratch/stefan/7774842/working/building/REAL300004517120 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 151) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/151 `/scratch/stefan/7774842/working/3D/151' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C(=O)[O-])C(=O)NCC1=CC=C(N2CCCC2)C=C1) `REAL300004517120.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517120/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517120 none CCCC(C(=O)[O-])C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 197, 156, 87, 156, 164, 164, 87, 87, 17, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201, 201, 201, 201, 197, 197, 156, 87, 17, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 201 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 43, 44]) total number of confs: 880 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517120 none CCCC(C(=O)[O-])C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [112, 107, 63, 24, 63, 69, 69, 24, 24, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 112, 112, 112, 112, 112, 107, 107, 63, 24, 5, 5, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1] 201 rigid atoms, others: [33, 34, 43, 44, 10, 11, 12, 13, 14, 15, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 523 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517120 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517120 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517120/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517120 Building REAL300004517121 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517121' /scratch/stefan/7774842/working/building/REAL300004517121 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517121 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517121/0 /scratch/stefan/7774842/working/building/REAL300004517121 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 152) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/152 `/scratch/stefan/7774842/working/3D/152' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1C(=O)NCC1=CC=C(N2CCCC2)C=C1) `REAL300004517121.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517121/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517121 none CC1=CC(C(=O)[O-])=CC=C1C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 81, 55, 77, 81, 81, 81, 81, 25, 25, 25, 4, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 1, 1, 81, 81, 81, 81, 81, 81, 25, 4, 4, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1] 192 rigid atoms, others: [34, 35, 45, 44, 13, 14, 15, 16, 17, 18, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 262 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517121 none CC1=CC(C(=O)[O-])=CC=C1C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 48, 81, 81, 48, 48, 171, 192, 192, 171, 81, 81, 2, 2, 2, 1, 1, 1, 10, 48, 48, 81, 81, 173, 171, 192, 192, 192, 192, 171, 178, 81, 81] 192 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 558 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517121 none CC1=CC(C(=O)[O-])=CC=C1C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [192, 192, 192, 163, 192, 192, 192, 192, 192, 85, 85, 85, 22, 4, 2, 7, 7, 1, 1, 1, 1, 1, 1, 7, 7, 192, 192, 192, 192, 192, 192, 85, 22, 22, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 192 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 44, 45]) total number of confs: 544 number of broken/clashed sets: 8 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517121 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517121 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517121/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517121 Building REAL300004517122 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517122' /scratch/stefan/7774842/working/building/REAL300004517122 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517122 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517122/0 /scratch/stefan/7774842/working/building/REAL300004517122 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 153) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/153 `/scratch/stefan/7774842/working/3D/153' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C(Cl)=C1) `REAL300004517122.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517122.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517122/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517122 none O=C([O-])C1=CC=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 16, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 53, 65, 65, 25, 25, 25, 4, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 1, 1, 65, 65, 65, 65, 65, 25, 4, 4, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 65] 158 rigid atoms, others: [40, 41, 10, 11, 12, 13, 14, 15, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 42]) total number of confs: 180 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517122 none O=C([O-])C1=CC=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 16, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 35, 65, 65, 35, 35, 143, 158, 158, 145, 65, 65, 1, 1, 1, 1, 1, 7, 35, 35, 65, 65, 147, 149, 158, 158, 158, 158, 143, 156, 65, 65, 1] 158 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 42, 22, 23, 24, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 490 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517122 none O=C([O-])C1=CC=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 16, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [158, 158, 158, 158, 158, 158, 85, 85, 85, 22, 4, 2, 7, 7, 1, 1, 1, 1, 1, 1, 7, 7, 158, 158, 158, 158, 158, 85, 22, 22, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 158] 158 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 40, 41, 42]) total number of confs: 373 number of broken/clashed sets: 10 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517122 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517122 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517122/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517122 Building REAL300004517123 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517123' /scratch/stefan/7774842/working/building/REAL300004517123 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517123 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517123/0 /scratch/stefan/7774842/working/building/REAL300004517123 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 154) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/154 `/scratch/stefan/7774842/working/3D/154' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1CC2(C1)CC(C(=O)NCC1=CC=C(N3CCCC3)C=C1)C2) `REAL300004517123.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517123.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517123/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517123 none O=C([O-])C1CC2(C1)CC(C(=O)NCC1=CC=C(N3CCCC3)C=C1)C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [89, 72, 89, 72, 72, 72, 72, 72, 19, 19, 19, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 72, 72, 72, 72, 72, 72, 72, 72, 72, 19, 3, 3, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 72, 72] 201 rigid atoms, others: [36, 37, 12, 13, 14, 15, 16, 17, 46, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 48, 49]) total number of confs: 261 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517123 none O=C([O-])C1CC2(C1)CC(C(=O)NCC1=CC=C(N3CCCC3)C=C1)C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 42, 72, 72, 42, 42, 190, 201, 201, 191, 72, 72, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 42, 42, 72, 72, 201, 187, 201, 201, 201, 201, 189, 201, 72, 72, 1, 1] 201 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 48, 49, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 532 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517123 none O=C([O-])C1CC2(C1)CC(C(=O)NCC1=CC=C(N3CCCC3)C=C1)C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 68, 68, 68, 13, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201, 201, 201, 201, 201, 201, 201, 201, 68, 13, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201] 201 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 46, 47, 48, 49]) total number of confs: 570 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517123 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517123 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517123/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517123 Building REAL300004517124 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517124' /scratch/stefan/7774842/working/building/REAL300004517124 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517124 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517124/0 /scratch/stefan/7774842/working/building/REAL300004517124 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 155) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/155 `/scratch/stefan/7774842/working/3D/155' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)[O-])=NC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=C1) `REAL300004517124.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517124.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517124/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517124 none COC1=CC(C(=O)[O-])=NC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [95, 64, 64, 64, 64, 64, 65, 65, 64, 27, 27, 27, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 64, 95, 95, 95, 64, 27, 4, 4, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 64] 201 rigid atoms, others: [33, 34, 43, 44, 13, 14, 15, 16, 17, 18, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 45]) total number of confs: 200 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517124 none COC1=CC(C(=O)[O-])=NC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 3, 3, 3, 19, 64, 64, 19, 21, 201, 201, 201, 201, 64, 64, 1, 3, 3, 3, 1, 3, 19, 19, 64, 64, 201, 173, 201, 201, 201, 201, 171, 201, 64, 64, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 8, 9, 10, 45, 25, 29] set([0, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 480 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517124 none COC1=CC(C(=O)[O-])=NC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 101, 101, 101, 17, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201, 201, 201, 201, 101, 17, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 201] 201 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 43, 44, 45]) total number of confs: 438 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517124 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517124 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517124/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517124 Building REAL300004517125 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517125' /scratch/stefan/7774842/working/building/REAL300004517125 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517125 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517125/0 /scratch/stefan/7774842/working/building/REAL300004517125 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 156) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/156 `/scratch/stefan/7774842/working/3D/156' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(C(=O)[O-])=CC=C1C(=O)NCC1=CC=C(N2CCCC2)C=C1) `REAL300004517125.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517125.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517125/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517125 none CN1C(C(=O)[O-])=CC=C1C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 11, 11, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 81, 81, 81, 81, 81, 81, 27, 26, 27, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 81, 81, 81, 81, 81, 26, 4, 4, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1] 182 rigid atoms, others: [32, 33, 42, 43, 12, 13, 14, 15, 16, 17, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 151 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517125 none CN1C(C(=O)[O-])=CC=C1C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 11, 11, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 12, 12, 12, 50, 81, 81, 50, 50, 168, 169, 169, 168, 81, 81, 2, 2, 2, 1, 1, 12, 50, 50, 81, 81, 168, 168, 178, 182, 175, 181, 168, 168, 81, 81] 182 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 9, 27, 28] set([4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 553 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517125 none CN1C(C(=O)[O-])=CC=C1C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 11, 11, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [182, 182, 182, 182, 182, 182, 182, 182, 95, 95, 95, 17, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 182, 182, 182, 182, 182, 95, 17, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 182 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 42, 43]) total number of confs: 389 number of broken/clashed sets: 15 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517125 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517125 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517125/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517125 Building REAL300004517126 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517126' /scratch/stefan/7774842/working/building/REAL300004517126 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517126 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517126/0 /scratch/stefan/7774842/working/building/REAL300004517126 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 157) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/157 `/scratch/stefan/7774842/working/3D/157' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1(C(=O)NCC2=CC=C(N3CCCC3)C=C2)CC=CC1) `REAL300004517126.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517126.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517126/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517126 none O=C([O-])C1(C(=O)NCC2=CC=C(N3CCCC3)C=C2)CC=CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [95, 69, 95, 26, 26, 26, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 1, 69, 69, 69, 69, 26, 4, 4, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 69, 69, 69, 69, 69, 69] 201 rigid atoms, others: [36, 37, 7, 8, 9, 10, 11, 12, 17, 18, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43]) total number of confs: 307 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517126 none O=C([O-])C1(C(=O)NCC2=CC=C(N3CCCC3)C=C2)CC=CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 4, 4, 4, 22, 69, 69, 22, 22, 201, 201, 201, 201, 69, 69, 1, 1, 1, 1, 4, 22, 22, 69, 69, 201, 175, 201, 201, 201, 201, 182, 201, 69, 69, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 3, 4, 38, 39, 40, 41, 42, 43, 19, 20, 21, 22] set([0, 2, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 480 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517126 none O=C([O-])C1(C(=O)NCC2=CC=C(N3CCCC3)C=C2)CC=CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 91, 91, 91, 18, 4, 3, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 201, 201, 201, 201, 91, 18, 18, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [32, 33, 34, 35, 11, 12, 13, 14, 15, 16, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 604 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517126 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517126 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517126/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517126 Building REAL300004517127 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517127' /scratch/stefan/7774842/working/building/REAL300004517127 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517127 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517127/0 /scratch/stefan/7774842/working/building/REAL300004517127 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 158) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/158 `/scratch/stefan/7774842/working/3D/158' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CCC1=CC=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C1) `REAL300004517127.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517127.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517127/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517127 none O=C([O-])CCC1=CC=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 87, 102, 61, 59, 59, 59, 59, 22, 22, 22, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 59, 59, 87, 87, 61, 61, 59, 59, 22, 4, 4, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 59, 59] 201 rigid atoms, others: [45, 35, 36, 12, 13, 14, 15, 16, 17, 46, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48]) total number of confs: 320 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517127 none O=C([O-])CCC1=CC=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 5, 7, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 29, 59, 59, 29, 46, 153, 153, 153, 153, 59, 59, 1, 1, 5, 5, 3, 3, 1, 1, 5, 29, 29, 59, 59, 153, 153, 153, 153, 153, 153, 147, 153, 59, 59, 1, 1] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 47, 48, 24, 25, 30, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 435 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517127 none O=C([O-])CCC1=CC=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 157, 153, 153, 153, 153, 69, 69, 69, 13, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 153, 153, 201, 201, 157, 157, 153, 153, 69, 13, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 153, 153] 201 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 45, 46, 47, 48]) total number of confs: 565 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517127 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517127 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517127/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517127 Building REAL300004517128 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517128' /scratch/stefan/7774842/working/building/REAL300004517128 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517128 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517128/0 /scratch/stefan/7774842/working/building/REAL300004517128 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 159) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/159 `/scratch/stefan/7774842/working/3D/159' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NNC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=C1C(=O)[O-]) `REAL300004517128.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517128.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517128/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517128 none CC1=NNC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 11, 11, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 189 conformations in input total number of sets (complete confs): 189 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 71, 28, 28, 28, 4, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 1, 1, 71, 71, 79, 79, 71, 71, 71, 71, 28, 4, 4, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1] 189 rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 18, 19, 41, 42, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 172 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517128 none CC1=NNC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 11, 11, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 189 conformations in input total number of sets (complete confs): 189 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 8, 8, 33, 71, 71, 33, 46, 189, 189, 189, 189, 71, 71, 1, 1, 3, 3, 2, 2, 2, 1, 8, 33, 33, 71, 71, 189, 188, 189, 189, 189, 189, 174, 189, 71, 71] 189 rigid atoms, others: [0, 1, 2, 3, 4, 5, 20, 21, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 473 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517128 none CC1=NNC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 11, 11, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 189 conformations in input total number of sets (complete confs): 189 using faster count positions algorithm for large data unique positions, atoms: [189, 189, 189, 189, 105, 105, 105, 20, 4, 2, 7, 7, 1, 1, 1, 1, 1, 1, 7, 7, 189, 189, 189, 189, 189, 189, 189, 189, 105, 20, 20, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 189 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 41, 42]) total number of confs: 427 number of broken/clashed sets: 6 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517128 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517128 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517128/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517128 Building REAL300004517129 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517129' /scratch/stefan/7774842/working/building/REAL300004517129 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517129 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517129/0 /scratch/stefan/7774842/working/building/REAL300004517129 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 160) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/160 `/scratch/stefan/7774842/working/3D/160' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1(CC(=O)NCC2=CC=C(N3CCCC3)C=C2)CC1) `REAL300004517129.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517129.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517129/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517129 none O=C([O-])CC1(CC(=O)NCC2=CC=C(N3CCCC3)C=C2)CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [96, 73, 96, 72, 58, 20, 20, 20, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 72, 72, 73, 73, 58, 58, 20, 4, 4, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 72, 72, 72, 72] 187 rigid atoms, others: [40, 9, 10, 11, 12, 13, 14, 19, 20, 41, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43, 44, 45]) total number of confs: 379 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517129 none O=C([O-])CC1(CC(=O)NCC2=CC=C(N3CCCC3)C=C2)CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [11, 5, 11, 1, 1, 1, 6, 12, 12, 12, 39, 72, 72, 39, 42, 187, 187, 187, 187, 72, 72, 1, 1, 5, 5, 6, 6, 12, 39, 39, 72, 72, 187, 178, 187, 187, 187, 187, 177, 187, 72, 72, 1, 1, 1, 1] 187 rigid atoms, others: [3, 4, 5, 42, 43, 44, 45, 21, 22] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 518 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517129 none O=C([O-])CC1(CC(=O)NCC2=CC=C(N3CCCC3)C=C2)CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [187, 187, 187, 187, 168, 67, 67, 67, 13, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 187, 187, 187, 187, 168, 168, 67, 13, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 187, 187, 187, 187] 187 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 40, 41, 42, 43, 44, 45]) total number of confs: 745 number of broken/clashed sets: 5 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517129 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517129 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517129/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517129 Building REAL300004517130 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517130' /scratch/stefan/7774842/working/building/REAL300004517130 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517130 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517130/0 /scratch/stefan/7774842/working/building/REAL300004517130 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 161) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/161 `/scratch/stefan/7774842/working/3D/161' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1C(F)(F)C12CC(C(=O)NCC1=CC=C(N3CCCC3)C=C1)C2) `REAL300004517130.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517130 none O=C([O-])C1C(F)(F)C12CC(C(=O)NCC1=CC=C(N3CCCC3)C=C1)C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 15, 15, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 94, 99, 94, 94, 94, 94, 94, 94, 23, 23, 23, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 94, 94, 94, 94, 94, 23, 5, 5, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 94, 94] 201 rigid atoms, others: [33, 34, 43, 44, 13, 14, 15, 16, 17, 18, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46]) total number of confs: 265 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517130 none O=C([O-])C1C(F)(F)C12CC(C(=O)NCC1=CC=C(N3CCCC3)C=C1)C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 15, 15, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 54, 94, 94, 54, 72, 201, 201, 201, 201, 94, 94, 1, 1, 1, 1, 1, 10, 54, 54, 94, 94, 201, 198, 201, 201, 201, 201, 193, 201, 94, 94, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 45, 46, 25, 26, 27, 28, 29] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 586 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517130 none O=C([O-])C1C(F)(F)C12CC(C(=O)NCC1=CC=C(N3CCCC3)C=C1)C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 15, 15, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 78, 78, 78, 14, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201, 201, 201, 201, 78, 14, 14, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201] 201 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 43, 44, 45, 46]) total number of confs: 553 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517130 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517130 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517130/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517130 Building REAL300004517131 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517131' /scratch/stefan/7774842/working/building/REAL300004517131 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517131 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517131/0 /scratch/stefan/7774842/working/building/REAL300004517131 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 162) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/162 `/scratch/stefan/7774842/working/3D/162' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=NC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=CS1) `REAL300004517131.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517131 none O=C([O-])C1=NC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [42, 41, 42, 41, 41, 23, 23, 23, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 41, 41, 23, 4, 4, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 42] 81 rigid atoms, others: [36, 37, 9, 10, 11, 12, 13, 14, 19, 20, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 38]) total number of confs: 102 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517131 none O=C([O-])C1=NC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 5, 5, 5, 22, 42, 42, 22, 22, 81, 81, 81, 77, 42, 42, 1, 1, 5, 21, 21, 42, 42, 81, 81, 81, 81, 81, 81, 77, 81, 42, 42, 1] 81 rigid atoms, others: [1, 3, 4, 5, 6, 21, 22, 38] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517131 none O=C([O-])C1=NC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 81, 81, 81, 77, 77, 77, 17, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 81, 81, 77, 17, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 81] 81 rigid atoms, others: [32, 33, 34, 35, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 36, 37, 38]) total number of confs: 220 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517131 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517131 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517131/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517131 Building REAL300004517132 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517132' /scratch/stefan/7774842/working/building/REAL300004517132 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517132 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517132/0 /scratch/stefan/7774842/working/building/REAL300004517132 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 163) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/163 `/scratch/stefan/7774842/working/3D/163' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]1(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C[C@H]1C(=O)[O-]) `REAL300004517132.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517132.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517132/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517132 none C[C@]1(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C[C@H]1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 5, 7, 1, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [54, 26, 26, 26, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 1, 54, 54, 54, 54, 73, 73, 54, 54, 54, 26, 4, 4, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 54, 54] 157 rigid atoms, others: [5, 6, 7, 8, 9, 10, 39, 15, 16, 40, 29, 30] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42]) total number of confs: 239 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517132 none C[C@]1(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C[C@H]1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 5, 7, 1, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 4, 4, 4, 21, 54, 54, 21, 21, 146, 157, 157, 148, 54, 54, 1, 1, 1, 1, 3, 3, 2, 2, 2, 4, 21, 21, 54, 54, 157, 140, 157, 157, 157, 157, 141, 157, 54, 54, 1, 1] 157 rigid atoms, others: [0, 1, 2, 41, 42, 17, 18, 19, 20] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 430 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517132 none C[C@]1(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C[C@H]1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 5, 7, 1, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 157 conformations in input total number of sets (complete confs): 157 using faster count positions algorithm for large data unique positions, atoms: [157, 90, 90, 90, 20, 4, 4, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 157, 157, 157, 157, 157, 157, 157, 157, 157, 90, 20, 20, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 157, 157] 157 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 39, 40, 41, 42]) total number of confs: 489 number of broken/clashed sets: 7 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517132 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517132 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517132/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517132 Building REAL300004517133 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517133' /scratch/stefan/7774842/working/building/REAL300004517133 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517133 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517133/0 /scratch/stefan/7774842/working/building/REAL300004517133 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 164) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/164 `/scratch/stefan/7774842/working/3D/164' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C(C(=O)[O-])S1) `REAL300004517133.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517133 none CC1=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 90, 26, 26, 26, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 90, 90, 90, 90, 90, 90, 90, 90, 90, 26, 5, 5, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 90] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 16, 17, 41, 40, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 42]) total number of confs: 158 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517133 none CC1=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 9, 9, 9, 48, 90, 90, 48, 67, 201, 201, 201, 201, 90, 90, 1, 1, 1, 2, 2, 1, 2, 2, 2, 9, 48, 48, 90, 90, 201, 200, 201, 201, 201, 201, 192, 201, 90, 90, 1] 201 rigid atoms, others: [0, 1, 2, 3, 42, 18, 19, 20, 23] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 588 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517133 none CC1=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 90, 90, 90, 17, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201, 201, 201, 201, 201, 201, 201, 201, 90, 17, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 40, 41, 42]) total number of confs: 419 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517133 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517133 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517133/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517133 Building REAL300004517134 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517134' /scratch/stefan/7774842/working/building/REAL300004517134 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517134 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517134/0 /scratch/stefan/7774842/working/building/REAL300004517134 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 165) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/165 `/scratch/stefan/7774842/working/3D/165' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=C(S1)SC(C(=O)NCC1=CC=C(N3CCCC3)C=C1)=C2) `REAL300004517134.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517134/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517134 none O=C([O-])C1=CC2=C(S1)SC(C(=O)NCC1=CC=C(N3CCCC3)C=C1)=C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 14, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 91, 91, 91, 91, 91, 91, 91, 25, 25, 25, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 91, 91, 25, 5, 5, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 91] 182 rigid atoms, others: [40, 41, 13, 14, 15, 16, 17, 18, 23, 24, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 42]) total number of confs: 157 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517134 none O=C([O-])C1=CC2=C(S1)SC(C(=O)NCC1=CC=C(N3CCCC3)C=C1)=C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 14, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 59, 91, 91, 59, 74, 182, 182, 182, 182, 91, 91, 1, 1, 13, 58, 58, 91, 91, 182, 179, 182, 182, 182, 182, 179, 182, 91, 91, 1] 182 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 42] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 533 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517134 none O=C([O-])C1=CC2=C(S1)SC(C(=O)NCC1=CC=C(N3CCCC3)C=C1)=C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 14, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [182, 182, 182, 182, 182, 182, 182, 182, 182, 85, 85, 85, 17, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 182, 182, 85, 17, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 182] 182 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 40, 41, 42]) total number of confs: 380 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517134 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517134 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517134/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517134 Building REAL300004517135 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517135' /scratch/stefan/7774842/working/building/REAL300004517135 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517135 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517135/0 /scratch/stefan/7774842/working/building/REAL300004517135 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 166) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/166 `/scratch/stefan/7774842/working/3D/166' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)[O-])=C(Cl)C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=C1) `REAL300004517135.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517135.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517135/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517135 none COC1=CC(C(=O)[O-])=C(Cl)C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 16, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [87, 71, 71, 71, 71, 71, 73, 73, 71, 71, 23, 23, 23, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 71, 87, 87, 87, 71, 23, 5, 5, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 71] 201 rigid atoms, others: [34, 35, 44, 45, 14, 15, 16, 17, 18, 19, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 46]) total number of confs: 170 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517135 none COC1=CC(C(=O)[O-])=C(Cl)C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 16, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 7, 7, 7, 38, 71, 71, 38, 51, 199, 199, 199, 199, 71, 71, 1, 3, 3, 3, 1, 7, 38, 38, 71, 71, 199, 198, 199, 199, 199, 199, 191, 199, 71, 71, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 8, 9, 10, 11, 46, 26, 30] set([0, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 498 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517135 none COC1=CC(C(=O)[O-])=C(Cl)C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 16, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 199, 199, 199, 199, 199, 201, 201, 199, 199, 70, 70, 70, 14, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 199, 201, 201, 201, 199, 70, 14, 14, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 199] 201 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 44, 45, 46]) total number of confs: 390 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517135 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517135 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517135/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517135 Building REAL300004517136 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517136' /scratch/stefan/7774842/working/building/REAL300004517136 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517136 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517136/0 /scratch/stefan/7774842/working/building/REAL300004517136 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 167) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/167 `/scratch/stefan/7774842/working/3D/167' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=CC(F)=C1C(=O)NCC1=CC=C(N2CCCC2)C=C1) `REAL300004517136.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517136 none CC1=C(C(=O)[O-])C=CC(F)=C1C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 15, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [84, 84, 84, 84, 85, 85, 84, 84, 84, 84, 20, 20, 20, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 85, 85, 85, 84, 84, 20, 3, 3, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1] 201 rigid atoms, others: [34, 35, 44, 45, 14, 15, 16, 17, 18, 19, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 146 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517136 none CC1=C(C(=O)[O-])C=CC(F)=C1C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 15, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 58, 84, 84, 58, 59, 199, 201, 201, 199, 84, 84, 2, 2, 2, 1, 1, 9, 58, 58, 84, 84, 201, 199, 201, 201, 201, 201, 199, 201, 84, 84] 201 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 9, 10, 11, 29, 30] set([4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 530 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517136 none CC1=C(C(=O)[O-])C=CC(F)=C1C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 15, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 68, 68, 68, 13, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201, 201, 201, 201, 68, 13, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 201 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 44, 45]) total number of confs: 361 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517136 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517136 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517136/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517136 Building REAL300004517137 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517137' /scratch/stefan/7774842/working/building/REAL300004517137 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517137 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517137/0 /scratch/stefan/7774842/working/building/REAL300004517137 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 168) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/168 `/scratch/stefan/7774842/working/3D/168' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C2C=C(C(=O)NCC3=CC=C(N4CCCC4)C=C3)SC2=CC=C1) `REAL300004517137.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517137.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517137/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517137 none O=C([O-])C1=C2C=C(C(=O)NCC3=CC=C(N4CCCC4)C=C3)SC2=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 14, 1, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [103, 88, 103, 88, 88, 88, 24, 24, 24, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 88, 88, 88, 88, 88, 88, 24, 5, 5, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 88, 88, 88] 201 rigid atoms, others: [32, 41, 10, 11, 12, 13, 14, 15, 20, 21, 42, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45]) total number of confs: 214 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517137 none O=C([O-])C1=C2C=C(C(=O)NCC3=CC=C(N4CCCC4)C=C3)SC2=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 14, 1, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 8, 8, 8, 45, 88, 88, 45, 61, 201, 201, 201, 201, 88, 88, 1, 1, 1, 1, 1, 1, 8, 45, 45, 88, 88, 201, 197, 201, 201, 201, 201, 188, 201, 88, 88, 1, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 43, 44, 45, 22, 23, 24, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 558 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517137 none O=C([O-])C1=C2C=C(C(=O)NCC3=CC=C(N4CCCC4)C=C3)SC2=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 14, 1, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 82, 82, 82, 16, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201, 201, 201, 201, 201, 82, 16, 16, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201, 201] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 41, 42, 43, 44, 45]) total number of confs: 398 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517137 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517137 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517137/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517137 Building REAL300004517138 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517138' /scratch/stefan/7774842/working/building/REAL300004517138 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517138 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517138/0 /scratch/stefan/7774842/working/building/REAL300004517138 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 169) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/169 `/scratch/stefan/7774842/working/3D/169' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=NC=CC=C1CCC(=O)NCC1=CC=C(N2CCCC2)C=C1) `REAL300004517138.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517138.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517138/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517138 none O=C([O-])C1=NC=CC=C1CCC(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [93, 93, 93, 93, 93, 93, 93, 93, 91, 74, 17, 17, 17, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 93, 93, 93, 91, 91, 74, 74, 17, 3, 3, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1] 201 rigid atoms, others: [36, 37, 14, 15, 16, 17, 18, 19, 46, 24, 25, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 371 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517138 none O=C([O-])C1=NC=CC=C1CCC(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 5, 8, 18, 18, 18, 60, 93, 93, 60, 60, 193, 201, 201, 192, 93, 93, 1, 1, 1, 5, 5, 8, 8, 18, 60, 60, 93, 93, 200, 194, 201, 201, 201, 201, 189, 201, 93, 93] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 26, 27, 28] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 619 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517138 none O=C([O-])C1=NC=CC=C1CCC(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 199, 180, 63, 63, 63, 13, 4, 3, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201, 201, 199, 199, 180, 180, 63, 13, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 201 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 46, 47]) total number of confs: 764 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517138 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517138 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517138/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517138 Building REAL300004517139 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517139' /scratch/stefan/7774842/working/building/REAL300004517139 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517139 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517139/0 /scratch/stefan/7774842/working/building/REAL300004517139 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 170) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/170 `/scratch/stefan/7774842/working/3D/170' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C12CC(C(=O)NCC3=CC=C(N4CCCC4)C=C3)(C1)OC2) `REAL300004517139.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517139/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517139 none O=C([O-])C12CC(C(=O)NCC3=CC=C(N4CCCC4)C=C3)(C1)OC2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 12, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [97, 92, 97, 92, 92, 25, 25, 25, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 92, 92, 92, 92, 92, 25, 4, 4, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 92, 92, 92, 92] 201 rigid atoms, others: [39, 40, 9, 10, 11, 12, 13, 14, 19, 20, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44]) total number of confs: 173 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517139 none O=C([O-])C12CC(C(=O)NCC3=CC=C(N4CCCC4)C=C3)(C1)OC2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 12, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 13, 13, 63, 92, 92, 63, 63, 198, 201, 201, 198, 92, 92, 1, 1, 1, 1, 1, 13, 63, 63, 92, 92, 201, 195, 201, 201, 201, 201, 198, 201, 92, 92, 1, 1, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 41, 42, 43, 44, 21, 22, 23, 24, 25] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 544 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517139 none O=C([O-])C12CC(C(=O)NCC3=CC=C(N4CCCC4)C=C3)(C1)OC2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 12, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 80, 80, 80, 14, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201, 201, 201, 201, 80, 14, 14, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201, 201, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 39, 40, 41, 42, 43, 44]) total number of confs: 387 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517139 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517139 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517139/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517139 Building REAL300004517140 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517140' /scratch/stefan/7774842/working/building/REAL300004517140 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517140 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517140/0 /scratch/stefan/7774842/working/building/REAL300004517140 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 171) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/171 `/scratch/stefan/7774842/working/3D/171' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(/C=C/C(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C1) `REAL300004517140.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517140.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517140/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517140 none O=C([O-])C1=CC=C(/C=C/C(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [112, 112, 112, 101, 112, 112, 91, 93, 25, 25, 25, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 112, 112, 112, 112, 96, 96, 25, 4, 4, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 112, 112] 201 rigid atoms, others: [33, 34, 44, 43, 12, 13, 14, 15, 16, 17, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46]) total number of confs: 353 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517140 none O=C([O-])C1=CC=C(/C=C/C(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 3, 3, 18, 18, 18, 71, 114, 114, 71, 71, 196, 201, 201, 201, 114, 114, 1, 1, 1, 1, 3, 3, 18, 71, 71, 114, 114, 201, 196, 201, 201, 201, 201, 201, 201, 114, 114, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 45, 46, 24, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 628 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517140 none O=C([O-])C1=CC=C(/C=C/C(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 193, 197, 83, 83, 83, 17, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201, 201, 201, 201, 201, 83, 17, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201] 201 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 43, 44, 45, 46]) total number of confs: 598 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517140 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517140 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517140/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517140 Building REAL300004517141 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517141' /scratch/stefan/7774842/working/building/REAL300004517141 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517141 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517141/0 /scratch/stefan/7774842/working/building/REAL300004517141 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 172) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/172 `/scratch/stefan/7774842/working/3D/172' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC1(C(=O)[O-])C(=O)NCC1=CC=C(N2CCCC2)C=C1) `REAL300004517141.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517141.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517141/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517141 none CC1CC1(C(=O)[O-])C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 170 conformations in input total number of sets (complete confs): 170 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 77, 26, 77, 84, 84, 26, 26, 4, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 1, 1, 77, 77, 77, 77, 77, 77, 26, 4, 4, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1] 170 rigid atoms, others: [32, 41, 10, 11, 12, 13, 14, 15, 20, 21, 42, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 249 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517141 none CC1CC1(C(=O)[O-])C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 170 conformations in input total number of sets (complete confs): 170 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 1, 5, 5, 5, 29, 77, 77, 29, 29, 155, 170, 170, 159, 77, 77, 2, 2, 2, 1, 1, 1, 5, 29, 29, 77, 77, 170, 156, 170, 170, 170, 170, 159, 170, 77, 77] 170 rigid atoms, others: [0, 1, 2, 3, 4, 7, 25, 26, 27] set([5, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 533 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517141 none CC1CC1(C(=O)[O-])C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 170 conformations in input total number of sets (complete confs): 170 using faster count positions algorithm for large data unique positions, atoms: [170, 170, 170, 92, 170, 170, 170, 92, 92, 22, 3, 2, 8, 8, 1, 1, 1, 1, 1, 1, 8, 8, 170, 170, 170, 170, 170, 170, 92, 22, 22, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 170 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 41, 42]) total number of confs: 533 number of broken/clashed sets: 8 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517141 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517141 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517141/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517141 Building REAL300004517142 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517142' /scratch/stefan/7774842/working/building/REAL300004517142 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517142 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517142/0 /scratch/stefan/7774842/working/building/REAL300004517142 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 173) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/173 `/scratch/stefan/7774842/working/3D/173' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1(C(=O)NCC2=CC=C(N3CCCC3)C=C2)CC2(CCC2)C1) `REAL300004517142.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517142.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517142/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517142 none O=C([O-])C1(C(=O)NCC2=CC=C(N3CCCC3)C=C2)CC2(CCC2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [112, 72, 112, 28, 28, 28, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 1, 72, 72, 72, 72, 72, 72, 28, 5, 5, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 72, 72, 72, 72, 72, 72, 72, 72, 72, 72] 201 rigid atoms, others: [38, 7, 8, 9, 10, 11, 12, 17, 18, 39, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 372 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517142 none O=C([O-])C1(C(=O)NCC2=CC=C(N3CCCC3)C=C2)CC2(CCC2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 5, 5, 5, 24, 72, 72, 36, 36, 201, 201, 201, 201, 72, 72, 1, 1, 1, 1, 1, 1, 5, 24, 24, 72, 72, 201, 201, 201, 201, 201, 201, 201, 201, 72, 72, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [1, 3, 4, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 20, 21, 22, 23, 24] set([0, 2, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 430 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517142 none O=C([O-])C1(C(=O)NCC2=CC=C(N3CCCC3)C=C2)CC2(CCC2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 99, 99, 99, 18, 4, 4, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 201, 201, 201, 201, 201, 201, 99, 18, 18, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 603 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517142 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517142 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517142/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517142 Building REAL300004517143 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517143' /scratch/stefan/7774842/working/building/REAL300004517143 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517143 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517143/0 /scratch/stefan/7774842/working/building/REAL300004517143 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 174) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/174 `/scratch/stefan/7774842/working/3D/174' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=CC(C(=O)[O-])=C1C(=O)NCC1=CC=C(N2CCCC2)C=C1) `REAL300004517143.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517143.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517143/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517143 none CN1N=CC(C(=O)[O-])=C1C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 11, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 72, 72, 72, 96, 96, 26, 26, 26, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 72, 72, 72, 72, 26, 5, 5, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1] 201 rigid atoms, others: [32, 41, 42, 12, 13, 14, 15, 16, 17, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 237 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517143 none CN1N=CC(C(=O)[O-])=C1C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 11, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 6, 6, 6, 30, 72, 72, 30, 30, 174, 201, 201, 172, 72, 72, 2, 2, 2, 1, 6, 30, 30, 72, 72, 193, 176, 201, 201, 201, 201, 173, 201, 72, 72] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 8, 9, 27] set([6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 627 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517143 none CN1N=CC(C(=O)[O-])=C1C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 11, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 97, 97, 97, 17, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201, 201, 201, 97, 17, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 41, 42]) total number of confs: 424 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517143 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517143 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517143/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517143 Building REAL300004517144 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517144' /scratch/stefan/7774842/working/building/REAL300004517144 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517144 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517144/0 /scratch/stefan/7774842/working/building/REAL300004517144 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 175) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/175 `/scratch/stefan/7774842/working/3D/175' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CSC2=C1NC(C(=O)NCC1=CC=C(N3CCCC3)C=C1)=C2) `REAL300004517144.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517144.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517144/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517144 none O=C([O-])C1=CSC2=C1NC(C(=O)NCC1=CC=C(N3CCCC3)C=C1)=C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 80, 80, 80, 80, 80, 80, 80, 26, 26, 26, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 80, 80, 80, 26, 5, 5, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 80] 201 rigid atoms, others: [32, 41, 42, 13, 14, 15, 16, 17, 18, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 43]) total number of confs: 148 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517144 none O=C([O-])C1=CSC2=C1NC(C(=O)NCC1=CC=C(N3CCCC3)C=C1)=C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 60, 80, 80, 60, 73, 201, 201, 201, 201, 80, 80, 1, 1, 1, 11, 60, 60, 80, 80, 201, 199, 201, 201, 201, 201, 196, 201, 80, 80, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 43, 25, 26, 27] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 508 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517144 none O=C([O-])C1=CSC2=C1NC(C(=O)NCC1=CC=C(N3CCCC3)C=C1)=C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 93, 93, 93, 17, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201, 201, 93, 17, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 201] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 41, 42, 43]) total number of confs: 417 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517144 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517144 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517144/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517144 Building REAL300004517145 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517145' /scratch/stefan/7774842/working/building/REAL300004517145 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517145 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517145/0 /scratch/stefan/7774842/working/building/REAL300004517145 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 176) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/176 `/scratch/stefan/7774842/working/3D/176' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=C(C=C(C(=O)NCC3=CC=C(N4CCCC4)C=C3)N2)S1) `REAL300004517145.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517145.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517145/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517145 none O=C([O-])C1=CC2=C(C=C(C(=O)NCC3=CC=C(N4CCCC4)C=C3)N2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 8, 14, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 80, 80, 80, 80, 80, 80, 26, 25, 26, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 80, 80, 80, 80, 25, 4, 4, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 80] 164 rigid atoms, others: [32, 41, 42, 12, 13, 14, 15, 16, 17, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 43]) total number of confs: 145 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517145 none O=C([O-])C1=CC2=C(C=C(C(=O)NCC3=CC=C(N4CCCC4)C=C3)N2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 8, 14, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 12, 12, 13, 53, 80, 80, 53, 53, 151, 164, 164, 151, 80, 80, 1, 1, 1, 1, 13, 53, 53, 80, 80, 157, 154, 164, 164, 164, 164, 159, 162, 80, 80, 1] 164 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 43, 24, 25, 26, 27] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 541 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517145 none O=C([O-])C1=CC2=C(C=C(C(=O)NCC3=CC=C(N4CCCC4)C=C3)N2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 8, 14, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [164, 164, 164, 164, 164, 164, 164, 164, 80, 80, 80, 17, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 164, 164, 164, 164, 80, 17, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 164] 164 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 41, 42, 43]) total number of confs: 357 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517145 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517145 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517145/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517145 Building REAL300004517146 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517146' /scratch/stefan/7774842/working/building/REAL300004517146 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517146 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517146/0 /scratch/stefan/7774842/working/building/REAL300004517146 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 177) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/177 `/scratch/stefan/7774842/working/3D/177' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=COC2=C1NC(C(=O)NCC1=CC=C(N3CCCC3)C=C1)=C2) `REAL300004517146.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517146.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517146/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517146 none O=C([O-])C1=COC2=C1NC(C(=O)NCC1=CC=C(N3CCCC3)C=C1)=C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 12, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [76, 75, 76, 75, 75, 75, 75, 75, 75, 25, 25, 25, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 75, 75, 75, 25, 4, 4, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 75] 201 rigid atoms, others: [32, 41, 42, 13, 14, 15, 16, 17, 18, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 43]) total number of confs: 143 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517146 none O=C([O-])C1=COC2=C1NC(C(=O)NCC1=CC=C(N3CCCC3)C=C1)=C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 12, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 55, 75, 75, 55, 55, 190, 201, 201, 194, 75, 75, 1, 1, 1, 12, 55, 55, 75, 75, 201, 188, 201, 201, 201, 201, 193, 201, 75, 75, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 43, 25, 26, 27] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 533 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517146 none O=C([O-])C1=COC2=C1NC(C(=O)NCC1=CC=C(N3CCCC3)C=C1)=C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 12, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 87, 87, 87, 17, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201, 201, 87, 17, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 201] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 41, 42, 43]) total number of confs: 419 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517146 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517146 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517146/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517146 Building REAL300004517147 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517147' /scratch/stefan/7774842/working/building/REAL300004517147 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517147 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517147/0 /scratch/stefan/7774842/working/building/REAL300004517147 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 178) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/178 `/scratch/stefan/7774842/working/3D/178' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=CC=C1C(=O)NCC1=CC=C(N2CCCC2)C=C1) `REAL300004517147.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517147 none CC1=C(C(=O)[O-])C=CC=C1C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [89, 89, 89, 89, 89, 89, 89, 89, 89, 23, 23, 23, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 1, 89, 89, 89, 89, 89, 89, 23, 4, 4, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1] 201 rigid atoms, others: [34, 35, 45, 44, 13, 14, 15, 16, 17, 18, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 152 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517147 none CC1=C(C(=O)[O-])C=CC=C1C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 10, 10, 10, 50, 89, 89, 50, 56, 201, 201, 201, 201, 89, 89, 2, 2, 2, 1, 1, 1, 10, 50, 50, 89, 89, 201, 187, 201, 201, 201, 201, 189, 201, 89, 89] 201 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 9, 10, 28, 29, 30] set([4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 585 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517147 none CC1=C(C(=O)[O-])C=CC=C1C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 85, 85, 85, 19, 4, 4, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 201, 201, 201, 201, 201, 201, 85, 19, 19, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 201 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 44, 45]) total number of confs: 414 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517147 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517147 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517147/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517147 Building REAL300004517148 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517148' /scratch/stefan/7774842/working/building/REAL300004517148 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517148 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517148/0 /scratch/stefan/7774842/working/building/REAL300004517148 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 179) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/179 `/scratch/stefan/7774842/working/3D/179' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=CC(=O)NCC2=CC=C(N3CCCC3)C=C2)C=N1) `REAL300004517148.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517148/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517148 none O=C([O-])C1=CC=C(C=CC(=O)NCC2=CC=C(N3CCCC3)C=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [120, 120, 120, 120, 120, 120, 63, 62, 18, 18, 18, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 120, 120, 120, 120, 63, 63, 18, 3, 3, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 120] 201 rigid atoms, others: [33, 34, 44, 43, 12, 13, 14, 15, 16, 17, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 45]) total number of confs: 269 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517148 none O=C([O-])C1=CC=C(C=CC(=O)NCC2=CC=C(N3CCCC3)C=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 5, 5, 21, 21, 21, 90, 120, 120, 90, 90, 200, 201, 201, 200, 120, 120, 1, 1, 1, 1, 5, 5, 21, 90, 90, 120, 120, 201, 201, 201, 201, 201, 201, 200, 201, 120, 120, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 45, 24, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 628 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517148 none O=C([O-])C1=CC=C(C=CC(=O)NCC2=CC=C(N3CCCC3)C=C2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 139, 139, 55, 55, 55, 13, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201, 201, 201, 139, 139, 55, 13, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 201] 201 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 43, 44, 45]) total number of confs: 522 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517148 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517148 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517148/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517148 Building REAL300004517149 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517149' /scratch/stefan/7774842/working/building/REAL300004517149 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517149 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517149/0 /scratch/stefan/7774842/working/building/REAL300004517149 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 180) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/180 `/scratch/stefan/7774842/working/3D/180' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CCC1(C(=O)[O-])C(=O)NCC1=CC=C(N2CCCC2)C=C1) `REAL300004517149.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517149.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517149/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517149 none C=C1CCC1(C(=O)[O-])C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 11, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 76, 76, 27, 76, 122, 122, 27, 27, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 1, 1, 76, 76, 76, 76, 76, 76, 27, 4, 4, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1] 201 rigid atoms, others: [32, 33, 43, 42, 11, 12, 13, 14, 15, 16, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 401 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517149 none C=C1CCC1(C(=O)[O-])C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 11, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 1, 5, 5, 5, 27, 76, 76, 27, 27, 155, 201, 201, 155, 76, 76, 1, 1, 1, 1, 1, 1, 5, 27, 27, 76, 76, 155, 155, 201, 201, 201, 201, 155, 155, 76, 76] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 8, 23, 24, 25, 26, 27, 28] set([6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 551 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517149 none C=C1CCC1(C(=O)[O-])C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 11, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 90, 201, 201, 201, 90, 90, 18, 4, 3, 6, 6, 1, 1, 1, 1, 1, 1, 6, 6, 201, 201, 201, 201, 201, 201, 90, 18, 18, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 42, 43]) total number of confs: 600 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517149 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517149 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517149/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517149 Building REAL300004517150 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517150' /scratch/stefan/7774842/working/building/REAL300004517150 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517150 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517150/0 /scratch/stefan/7774842/working/building/REAL300004517150 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 181) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/181 `/scratch/stefan/7774842/working/3D/181' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CSC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=C1) `REAL300004517150.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517150/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517150 none O=C([O-])C1=CSC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [85, 84, 84, 84, 84, 84, 26, 26, 26, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 84, 84, 26, 4, 4, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 84] 201 rigid atoms, others: [37, 38, 10, 11, 12, 13, 14, 15, 20, 21, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 39]) total number of confs: 155 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517150 none O=C([O-])C1=CSC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 57, 85, 85, 57, 57, 185, 201, 201, 185, 85, 85, 1, 1, 12, 56, 56, 85, 85, 185, 185, 201, 201, 201, 201, 185, 185, 85, 85, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 39, 22, 23] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 525 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517150 none O=C([O-])C1=CSC(C(=O)NCC2=CC=C(N3CCCC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 88, 88, 88, 17, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201, 88, 17, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 37, 38, 39]) total number of confs: 416 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517150 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517150 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517150/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517150 Building REAL300004517151 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517151' /scratch/stefan/7774842/working/building/REAL300004517151 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517151 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517151/0 /scratch/stefan/7774842/working/building/REAL300004517151 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 182) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/182 `/scratch/stefan/7774842/working/3D/182' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])[C@H]1[C@@H]2CC[C@@H](O2)[C@H]1C(=O)NCC1=CC=C(N2CCCC2)C=C1) `REAL300004517151.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517151/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517151 none O=C([O-])[C@H]1[C@@H]2CC[C@@H](O2)[C@H]1C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 7, 5, 5, 5, 7, 12, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [39, 38, 39, 38, 38, 38, 38, 38, 38, 38, 38, 38, 23, 38, 23, 23, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 38, 38, 38, 38, 23, 5, 5, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1] 74 rigid atoms, others: [36, 37, 46, 47, 17, 18, 19, 20, 21, 22, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 117 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517151 none O=C([O-])[C@H]1[C@@H]2CC[C@@H](O2)[C@H]1C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 7, 5, 5, 5, 7, 12, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 19, 38, 38, 23, 19, 63, 63, 63, 63, 38, 38, 1, 1, 1, 1, 6, 19, 19, 38, 38, 63, 63, 63, 63, 63, 63, 63, 63, 38, 38] 74 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 29, 30, 31] set([0, 2, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 189 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517151 none O=C([O-])[C@H]1[C@@H]2CC[C@@H](O2)[C@H]1C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 7, 5, 5, 5, 7, 12, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [74, 74, 74, 74, 74, 74, 74, 74, 74, 74, 74, 74, 59, 74, 59, 59, 17, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 74, 74, 74, 74, 59, 17, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 74 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 46, 47]) total number of confs: 228 number of broken/clashed sets: 5 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517151 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517151 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517151/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517151 Building REAL300004517152 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517152' /scratch/stefan/7774842/working/building/REAL300004517152 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517152 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517152/0 /scratch/stefan/7774842/working/building/REAL300004517152 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 183) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/183 `/scratch/stefan/7774842/working/3D/183' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC2=C(C(=O)NCC3=CC=C(N4CCCC4)C=C3)C=CC=C12) `REAL300004517152.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517152 none O=C([O-])C1=CC=CC2=C(C(=O)NCC3=CC=C(N4CCCC4)C=C3)C=CC=C12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [108, 102, 108, 102, 102, 102, 102, 102, 26, 26, 26, 5, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 102, 102, 102, 102, 102, 102, 102, 26, 5, 5, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 102, 102, 102] 201 rigid atoms, others: [34, 35, 44, 45, 12, 13, 14, 15, 16, 17, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48]) total number of confs: 194 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517152 none O=C([O-])C1=CC=CC2=C(C(=O)NCC3=CC=C(N4CCCC4)C=C3)C=CC=C12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 52, 102, 102, 52, 54, 194, 201, 201, 197, 102, 102, 1, 1, 1, 1, 1, 1, 1, 9, 52, 52, 102, 102, 201, 186, 201, 201, 201, 201, 189, 201, 102, 102, 1, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 46, 47, 48, 24, 25, 26, 27, 28, 29, 30] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 621 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517152 none O=C([O-])C1=CC=CC2=C(C(=O)NCC3=CC=C(N4CCCC4)C=C3)C=CC=C12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 81, 81, 81, 15, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201, 201, 201, 201, 201, 201, 81, 15, 15, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201, 201] 201 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 44, 45, 46, 47, 48]) total number of confs: 389 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517152 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517152 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517152/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517152 Building REAL300004517153 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517153' /scratch/stefan/7774842/working/building/REAL300004517153 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517153 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517153/0 /scratch/stefan/7774842/working/building/REAL300004517153 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 184) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/184 `/scratch/stefan/7774842/working/3D/184' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@]1(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C[C@H]1C(=O)[O-]) `REAL300004517153.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517153.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517153/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517153 none CC(C)[C@]1(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C[C@H]1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 5, 7, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [56, 28, 56, 21, 20, 21, 4, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 1, 1, 28, 28, 28, 28, 41, 41, 56, 56, 56, 56, 56, 56, 56, 20, 4, 4, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 28, 28] 151 rigid atoms, others: [35, 36, 7, 8, 9, 10, 11, 12, 45, 46, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48]) total number of confs: 271 number of broken/clashed sets: 55 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517153 none CC(C)[C@]1(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C[C@H]1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 5, 7, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 1, 1, 3, 3, 3, 11, 28, 28, 11, 12, 115, 115, 115, 115, 28, 28, 1, 1, 1, 1, 3, 3, 7, 7, 7, 7, 7, 7, 7, 3, 11, 11, 28, 28, 115, 103, 115, 115, 115, 115, 101, 115, 28, 28, 1, 1] 151 rigid atoms, others: [1, 3, 4, 47, 48, 19, 20, 21, 22] set([0, 2, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 270 number of broken/clashed sets: 55 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517153 none CC(C)[C@]1(C(=O)NCC2=CC=C(N3CCCC3)C=C2)C[C@H]1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 5, 7, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [151, 115, 151, 89, 89, 89, 22, 4, 4, 7, 7, 1, 1, 1, 1, 1, 1, 7, 7, 115, 115, 115, 115, 144, 144, 151, 151, 151, 151, 151, 151, 151, 89, 22, 22, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 115, 115] 151 rigid atoms, others: [43, 37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 45, 46, 47, 48]) total number of confs: 664 number of broken/clashed sets: 55 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517153 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517153 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517153/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517153 Building REAL300004517154 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517154' /scratch/stefan/7774842/working/building/REAL300004517154 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517154 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517154/0 /scratch/stefan/7774842/working/building/REAL300004517154 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 185) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/185 `/scratch/stefan/7774842/working/3D/185' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1CC(=O)NCC1=CC=C(N2CCCC2)C=C1) `REAL300004517154.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517154.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517154/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517154 none CC1=CC(C(=O)[O-])=CC=C1CC(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [84, 84, 84, 82, 84, 84, 84, 84, 84, 64, 20, 20, 20, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 84, 84, 84, 84, 84, 84, 64, 64, 20, 4, 4, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1] 201 rigid atoms, others: [48, 37, 38, 14, 15, 16, 17, 18, 19, 24, 25, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 295 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517154 none CC1=CC(C(=O)[O-])=CC=C1CC(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 52, 84, 84, 52, 69, 201, 201, 201, 201, 84, 84, 2, 2, 2, 1, 1, 1, 5, 5, 15, 52, 52, 84, 84, 201, 199, 201, 201, 201, 201, 198, 201, 84, 84] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 555 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517154 none CC1=CC(C(=O)[O-])=CC=C1CC(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 186, 201, 201, 201, 201, 201, 155, 69, 69, 69, 13, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201, 201, 201, 201, 201, 155, 155, 69, 13, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 201 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 47, 48]) total number of confs: 750 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517154 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517154 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517154/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517154 Building REAL300004517155 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517155' /scratch/stefan/7774842/working/building/REAL300004517155 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517155 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517155/0 /scratch/stefan/7774842/working/building/REAL300004517155 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 186) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/186 `/scratch/stefan/7774842/working/3D/186' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CSC(CC(=O)NCC2=CC=C(N3CCCC3)C=C2)=C1) `REAL300004517155.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517155.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517155/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517155 none O=C([O-])C1=CSC(CC(=O)NCC2=CC=C(N3CCCC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [94, 94, 94, 94, 94, 94, 56, 17, 17, 17, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 94, 94, 56, 56, 17, 3, 3, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 94] 201 rigid atoms, others: [40, 41, 11, 12, 13, 14, 15, 16, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 42]) total number of confs: 267 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517155 none O=C([O-])C1=CSC(CC(=O)NCC2=CC=C(N3CCCC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 23, 23, 23, 59, 94, 94, 59, 59, 200, 201, 201, 199, 94, 94, 1, 1, 7, 7, 23, 59, 59, 94, 94, 201, 200, 201, 201, 201, 201, 199, 201, 94, 94, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 42, 23, 24] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 571 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517155 none O=C([O-])C1=CSC(CC(=O)NCC2=CC=C(N3CCCC3)C=C2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 132, 52, 52, 52, 13, 4, 1, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201, 132, 132, 52, 13, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 201] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 40, 41, 42]) total number of confs: 630 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517155 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517155 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517155/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517155 Building REAL300004517156 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517156' /scratch/stefan/7774842/working/building/REAL300004517156 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517156 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517156/0 /scratch/stefan/7774842/working/building/REAL300004517156 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 187) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/187 `/scratch/stefan/7774842/working/3D/187' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(CC(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C1F) `REAL300004517156.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517156.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517156/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517156 none O=C([O-])C1=CC=C(CC(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [85, 81, 85, 81, 81, 81, 31, 17, 17, 17, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 81, 81, 81, 81, 81, 31, 31, 17, 3, 3, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 81] 201 rigid atoms, others: [33, 34, 43, 44, 11, 12, 13, 14, 15, 16, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 45]) total number of confs: 216 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517156 none O=C([O-])C1=CC=C(CC(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 6, 11, 11, 11, 49, 81, 81, 49, 49, 194, 201, 201, 193, 81, 81, 1, 1, 1, 1, 1, 6, 6, 11, 49, 49, 81, 81, 199, 196, 201, 201, 201, 201, 196, 201, 81, 81, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 45, 23, 24, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 564 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517156 none O=C([O-])C1=CC=C(CC(=O)NCC2=CC=C(N3CCCC3)C=C2)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 85, 55, 55, 55, 13, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201, 201, 201, 201, 85, 85, 55, 13, 13, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 201] 201 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 43, 44, 45]) total number of confs: 522 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517156 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517156 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517156/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517156 Building REAL300004517157 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517157' /scratch/stefan/7774842/working/building/REAL300004517157 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517157 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517157/0 /scratch/stefan/7774842/working/building/REAL300004517157 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 188) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/188 `/scratch/stefan/7774842/working/3D/188' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)[C@H](C(=O)[O-])[C@@H]1C(=O)NCC1=CC=C(N2CCCC2)C=C1) `REAL300004517157.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517157.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517157/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517157 none CC1(C)[C@H](C(=O)[O-])[C@@H]1C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 11, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 27, 21, 27, 21, 21, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 27, 27, 27, 27, 27, 27, 21, 4, 4, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1] 63 rigid atoms, others: [34, 35, 45, 44, 13, 14, 15, 16, 17, 18, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 84 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517157 none CC1(C)[C@H](C(=O)[O-])[C@@H]1C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 11, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 3, 3, 3, 13, 27, 27, 13, 15, 63, 63, 63, 63, 27, 27, 2, 2, 2, 2, 2, 2, 3, 13, 13, 27, 27, 63, 56, 63, 63, 63, 63, 58, 63, 27, 27] 63 rigid atoms, others: [0, 1, 2, 3, 4, 5, 8, 9, 10] set([6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 197 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517157 none CC1(C)[C@H](C(=O)[O-])[C@@H]1C(=O)NCC1=CC=C(N2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 11, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 63, 63, 63, 63, 63, 55, 63, 55, 55, 17, 4, 1, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 63, 63, 63, 63, 63, 63, 55, 17, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 63 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 44, 45]) total number of confs: 201 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517157 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517157 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517157/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517157 Building REAL300004517158 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517158' /scratch/stefan/7774842/working/building/REAL300004517158 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517158 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517158/0 /scratch/stefan/7774842/working/building/REAL300004517158 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 189) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/189 `/scratch/stefan/7774842/working/3D/189' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C2CCCCC2=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)S1) `REAL300004517158.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517158.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517158/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517158 none O=C([O-])C1=C2CCCCC2=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [102, 92, 102, 92, 92, 92, 92, 92, 92, 92, 24, 24, 24, 4, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 1, 92, 92, 92, 92, 92, 92, 92, 92, 92, 24, 4, 4, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1] 201 rigid atoms, others: [48, 49, 38, 39, 14, 15, 16, 17, 18, 19, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 197 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517158 none O=C([O-])C1=C2CCCCC2=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 46, 92, 92, 46, 50, 201, 201, 201, 201, 92, 92, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 46, 46, 92, 92, 201, 183, 201, 201, 201, 201, 190, 201, 92, 92] 201 rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 33, 26, 27, 28, 29, 30, 31] set([0, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 558 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517158 none O=C([O-])C1=C2CCCCC2=C(C(=O)NCC2=CC=C(N3CCCC3)C=C2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 5, 5, 5, 5, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 85, 85, 85, 17, 4, 4, 5, 5, 1, 1, 1, 1, 1, 1, 5, 5, 201, 201, 201, 201, 201, 201, 201, 201, 201, 85, 17, 17, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 201 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 48, 49]) total number of confs: 403 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517158 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517158 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517158/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517158 Building REAL300004517159 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517159' /scratch/stefan/7774842/working/building/REAL300004517159 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517159 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517159/0 /scratch/stefan/7774842/working/building/REAL300004517159 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 190) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/190 `/scratch/stefan/7774842/working/3D/190' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C12CCC(C(=O)NCC3=CC=C(N4CCCC4)C=C3)(CC1)CC2) `REAL300004517159.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517159/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517159 none O=C([O-])C12CCC(C(=O)NCC3=CC=C(N4CCCC4)C=C3)(CC1)CC2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [82, 27, 82, 27, 77, 77, 27, 27, 27, 4, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 1, 1, 77, 77, 77, 77, 77, 77, 77, 77, 27, 4, 4, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 77, 77, 77, 77, 77, 77, 77, 77] 116 rigid atoms, others: [33, 34, 43, 44, 10, 11, 12, 13, 14, 15, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 496 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517159 none O=C([O-])C12CCC(C(=O)NCC3=CC=C(N4CCCC4)C=C3)(CC1)CC2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 6, 6, 6, 31, 77, 77, 31, 34, 110, 116, 116, 116, 77, 77, 1, 1, 1, 1, 1, 1, 1, 1, 6, 31, 31, 77, 77, 116, 108, 116, 116, 116, 116, 112, 116, 77, 77, 1, 1, 1, 1, 1, 1, 1, 1] 116 rigid atoms, others: [1, 3, 4, 5, 6, 7, 22, 23, 24, 25, 26, 27, 28, 29, 45, 46, 47, 48, 49, 50, 51, 52] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 424 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517159 none O=C([O-])C12CCC(C(=O)NCC3=CC=C(N4CCCC4)C=C3)(CC1)CC2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 8, 5, 5, 5, 5, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [116, 101, 116, 101, 116, 116, 101, 101, 101, 21, 4, 2, 7, 7, 1, 1, 1, 1, 1, 1, 7, 7, 116, 116, 116, 116, 116, 116, 116, 116, 101, 21, 21, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 116, 116, 116, 116, 116, 116, 116, 116] 116 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 443 number of broken/clashed sets: 9 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517159 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517159 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517159/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517159 Building REAL300004517160 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517160' /scratch/stefan/7774842/working/building/REAL300004517160 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517160 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517160/0 /scratch/stefan/7774842/working/building/REAL300004517160 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 191) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/191 `/scratch/stefan/7774842/working/3D/191' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C1) `REAL300004517160.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517160/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517160 none O=C([O-])C1=CC=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 7, 3, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 3, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 7, 7] 10 rigid atoms, others: [39, 9, 10, 11, 12, 13, 14, 20, 21, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41]) total number of confs: 38 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517160 none O=C([O-])C1=CC=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 7, 10, 10, 10, 10, 10, 7, 7, 1, 1, 1, 1, 4, 7, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 7, 1, 1] 10 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 40, 41, 22, 23, 24, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517160 none O=C([O-])C1=CC=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [10, 8, 10, 9, 10, 10, 8, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 10, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 10, 10] 10 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 39, 40, 41]) total number of confs: 34 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517160 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517160 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517160/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517160 Building REAL300004517161 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517161' /scratch/stefan/7774842/working/building/REAL300004517161 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517161 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517161/0 /scratch/stefan/7774842/working/building/REAL300004517161 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 192) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/192 `/scratch/stefan/7774842/working/3D/192' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=CC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=C1) `REAL300004517161.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517161 none O=C([O-])COC1=CC=CC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [162, 125, 163, 40, 9, 9, 9, 9, 9, 3, 3, 3, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 9, 125, 125, 9, 9, 9, 3, 1, 1, 10, 10, 10, 11, 10, 11, 10, 11, 11, 11, 1, 9] 201 rigid atoms, others: [32, 33, 44, 12, 13, 14, 15, 16, 17, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45]) total number of confs: 554 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517161 none O=C([O-])COC1=CC=CC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 25, 45, 6, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 9, 48, 48, 48, 48, 48, 9, 9, 1, 25, 25, 1, 1, 1, 5, 9, 9, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 9, 1] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 45, 25, 28, 29, 30] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 209 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517161 none O=C([O-])COC1=CC=CC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [200, 201, 201, 126, 48, 48, 48, 48, 48, 20, 20, 20, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 48, 201, 201, 48, 48, 48, 20, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 48] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 44, 45]) total number of confs: 600 number of broken/clashed sets: 33 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517161 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517161 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517161/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517161 Building REAL300004517162 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517162' /scratch/stefan/7774842/working/building/REAL300004517162 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517162 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517162/0 /scratch/stefan/7774842/working/building/REAL300004517162 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 193) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/193 `/scratch/stefan/7774842/working/3D/193' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=C1) `REAL300004517162.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517162.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517162/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517162 none O=C([O-])C1=CC=CC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 3, 3, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 1, 1, 11, 11, 11, 11, 3, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 11] 23 rigid atoms, others: [40, 10, 11, 12, 13, 14, 15, 21, 22, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41]) total number of confs: 25 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517162 none O=C([O-])C1=CC=CC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 11, 11, 11, 11, 23, 23, 23, 23, 23, 11, 11, 1, 1, 1, 1, 7, 11, 11, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 11, 1] 23 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 41, 23, 24, 25, 26] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517162 none O=C([O-])C1=CC=CC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 12, 12, 12, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 23, 23, 23, 23, 12, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 23] 23 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 40, 41]) total number of confs: 43 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517162 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517162 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517162/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517162 Building REAL300004517163 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517163' /scratch/stefan/7774842/working/building/REAL300004517163 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517163 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517163/0 /scratch/stefan/7774842/working/building/REAL300004517163 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 194) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/194 `/scratch/stefan/7774842/working/3D/194' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)S1) `REAL300004517163.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517163.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517163/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517163 none O=C([O-])C1=CC=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 14, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 3, 3, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 13, 13, 13, 3, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1] 15 rigid atoms, others: [38, 9, 10, 11, 12, 13, 14, 20, 21, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 24 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517163 none O=C([O-])C1=CC=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 14, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 8, 9, 13, 13, 13, 13, 15, 15, 15, 15, 15, 13, 13, 1, 1, 1, 9, 13, 13, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 13] 15 rigid atoms, others: [1, 3, 4, 5, 6, 7, 22, 23, 24] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517163 none O=C([O-])C1=CC=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 14, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 15, 7, 7, 7, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 15, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5] 15 rigid atoms, others: [32, 33, 34, 35, 36, 37, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 38]) total number of confs: 27 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517163 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517163 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517163/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517163 Building REAL300004517164 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517164' /scratch/stefan/7774842/working/building/REAL300004517164 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517164 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517164/0 /scratch/stefan/7774842/working/building/REAL300004517164 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 195) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/195 `/scratch/stefan/7774842/working/3D/195' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=N1) `REAL300004517164.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517164/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517164 none O=C([O-])C1=CC=CC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 1, 1, 9, 9, 9, 9, 3, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1] 11 rigid atoms, others: [40, 10, 11, 12, 13, 14, 15, 21, 22, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 21 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517164 none O=C([O-])C1=CC=CC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 6, 9, 9, 9, 9, 11, 11, 11, 11, 11, 9, 9, 1, 1, 1, 1, 6, 9, 9, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 9] 11 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 23, 24, 25, 26] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 25 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517164 none O=C([O-])C1=CC=CC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 8, 8, 8, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 11, 11, 11, 11, 8, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6] 11 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 40]) total number of confs: 21 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517164 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517164 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517164/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517164 Building REAL300004517165 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517165' /scratch/stefan/7774842/working/building/REAL300004517165 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517165 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517165/0 /scratch/stefan/7774842/working/building/REAL300004517165 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 196) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/196 `/scratch/stefan/7774842/working/3D/196' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(SC1=CC=CC=C1C(=O)NC1=CC=C(N2CCCCC2)C=N1)C(=O)[O-]) `REAL300004517165.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517165 none CC(SC1=CC=CC=C1C(=O)NC1=CC=C(N2CCCCC2)C=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [40, 30, 13, 13, 13, 7, 13, 13, 3, 3, 3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 1, 1, 40, 41, 41, 40, 40, 40, 40, 13, 13, 13, 13, 3, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1] 49 rigid atoms, others: [48, 36, 37, 11, 12, 13, 14, 15, 16, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 132 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517165 none CC(SC1=CC=CC=C1C(=O)NC1=CC=C(N2CCCCC2)C=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [14, 7, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 13, 13, 13, 13, 28, 28, 28, 28, 28, 13, 13, 14, 15, 15, 14, 14, 14, 14, 1, 1, 1, 1, 9, 13, 13, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 13] 49 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 9, 34, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 90 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517165 none CC(SC1=CC=CC=C1C(=O)NC1=CC=C(N2CCCCC2)C=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [49, 42, 28, 28, 28, 20, 28, 28, 13, 13, 13, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 9, 9, 49, 49, 49, 49, 49, 49, 49, 28, 28, 28, 28, 13, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9] 49 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48]) total number of confs: 138 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517165 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517165 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517165/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517165 Building REAL300004517166 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517166' /scratch/stefan/7774842/working/building/REAL300004517166 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517166 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517166/0 /scratch/stefan/7774842/working/building/REAL300004517166 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 197) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/197 `/scratch/stefan/7774842/working/3D/197' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=CC=C1OCC(=O)[O-]) `REAL300004517166.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517166.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517166/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517166 none CCOC1=CC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 39, 9, 9, 9, 3, 3, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 1, 1, 9, 9, 9, 9, 58, 158, 171, 171, 59, 59, 59, 59, 59, 9, 3, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 9, 9, 158, 158] 201 rigid atoms, others: [36, 37, 8, 9, 10, 11, 12, 13, 48, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52]) total number of confs: 709 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517166 none CCOC1=CC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 8, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 9, 18, 18, 18, 18, 18, 9, 9, 1, 1, 1, 1, 9, 35, 61, 61, 19, 19, 19, 19, 19, 1, 5, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 9, 1, 1, 35, 35] 201 rigid atoms, others: [34, 3, 4, 5, 6, 2, 49, 50, 21, 22, 23, 24] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 51, 52]) total number of confs: 286 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517166 none CCOC1=CC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [78, 56, 18, 18, 18, 6, 6, 6, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 18, 18, 18, 18, 93, 185, 192, 192, 78, 78, 78, 78, 78, 18, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 18, 18, 185, 185] 201 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49, 50, 51, 52]) total number of confs: 772 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517166 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517166 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517166/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517166 Building REAL300004517167 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517167' /scratch/stefan/7774842/working/building/REAL300004517167 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517167 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517167/0 /scratch/stefan/7774842/working/building/REAL300004517167 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 198) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/198 `/scratch/stefan/7774842/working/3D/198' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(CCC(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C1) `REAL300004517167.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517167.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517167/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517167 none O=C([O-])C1=CC=C(CCC(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 47, 46, 47, 47, 33, 19, 3, 3, 3, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 47, 47, 47, 47, 33, 33, 19, 19, 3, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 47, 47] 63 rigid atoms, others: [33, 34, 11, 12, 13, 14, 15, 16, 22, 23, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47]) total number of confs: 181 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517167 none O=C([O-])C1=CC=C(CCC(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 6, 9, 31, 31, 31, 47, 47, 47, 47, 63, 63, 63, 63, 63, 47, 47, 1, 1, 1, 1, 6, 6, 9, 9, 31, 47, 47, 63, 63, 63, 63, 63, 63, 63, 63, 63, 63, 47, 1, 1] 63 rigid atoms, others: [1, 3, 4, 5, 6, 7, 46, 47, 24, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517167 none O=C([O-])C1=CC=C(CCC(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 63, 63, 63, 58, 51, 15, 15, 15, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 63, 63, 63, 63, 58, 58, 51, 51, 15, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 63, 63] 63 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 45, 46, 47]) total number of confs: 224 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517167 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517167 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517167/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517167 Building REAL300004517168 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517168' /scratch/stefan/7774842/working/building/REAL300004517168 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517168 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517168/0 /scratch/stefan/7774842/working/building/REAL300004517168 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 199) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/199 `/scratch/stefan/7774842/working/3D/199' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=CC=N1) `REAL300004517168.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517168.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517168/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517168 none O=C([O-])C1=CC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=CC=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 8, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 3, 3, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 1, 1, 10, 10, 10, 10, 3, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 10, 10] 22 rigid atoms, others: [38, 8, 9, 10, 11, 12, 13, 19, 20, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40]) total number of confs: 24 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517168 none O=C([O-])C1=CC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=CC=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 8, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 10, 10, 10, 10, 22, 22, 22, 22, 22, 10, 10, 1, 1, 1, 1, 6, 10, 10, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 10, 1, 1] 22 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 39, 40, 21, 22, 23, 24] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517168 none O=C([O-])C1=CC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=CC=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 8, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 12, 12, 12, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 22, 22, 22, 22, 12, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 22, 22] 22 rigid atoms, others: [32, 33, 34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 38, 39, 40]) total number of confs: 42 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517168 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517168 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517168/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517168 Building REAL300004517169 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517169' /scratch/stefan/7774842/working/building/REAL300004517169 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517169 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517169/0 /scratch/stefan/7774842/working/building/REAL300004517169 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 200) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/200 `/scratch/stefan/7774842/working/3D/200' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=CC(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C1) `REAL300004517169.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517169.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517169/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517169 none O=C([O-])C1=CC=C(C=CC(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 19, 28, 19, 28, 28, 19, 19, 3, 3, 3, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 28, 28, 28, 28, 19, 19, 3, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 28, 28] 28 rigid atoms, others: [32, 43, 11, 12, 13, 14, 15, 16, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45]) total number of confs: 134 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517169 none O=C([O-])C1=CC=C(C=CC(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 4, 4, 18, 18, 18, 26, 26, 26, 26, 27, 27, 27, 27, 27, 26, 26, 1, 1, 1, 1, 4, 4, 18, 26, 26, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 26, 1, 1] 27 rigid atoms, others: [1, 3, 4, 5, 6, 7, 44, 45, 24, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 63 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517169 none O=C([O-])C1=CC=C(C=CC(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 28, 12, 12, 12, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 28, 28, 28, 28, 28, 28, 12, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 28, 28] 28 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 43, 44, 45]) total number of confs: 69 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517169 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517169 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517169/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517169 Building REAL300004517170 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517170' /scratch/stefan/7774842/working/building/REAL300004517170 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517170 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517170/0 /scratch/stefan/7774842/working/building/REAL300004517170 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 201) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/201 `/scratch/stefan/7774842/working/3D/201' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=CC([N+](=O)[O-])=C1) `REAL300004517170.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517170.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517170/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517170 none O=C([O-])C1=CC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 8, 11, 11, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 1, 1, 11, 11, 11, 11, 11, 11, 11, 3, 1, 1, 6, 6, 6, 7, 6, 6, 6, 7, 6, 6, 1, 11, 11] 20 rigid atoms, others: [8, 9, 10, 11, 12, 13, 19, 20, 41, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43]) total number of confs: 27 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517170 none O=C([O-])C1=CC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 8, 11, 11, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 7, 7, 7, 11, 11, 11, 11, 20, 20, 20, 20, 20, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 11, 1, 1] 20 rigid atoms, others: [1, 3, 4, 5, 6, 42, 43, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517170 none O=C([O-])C1=CC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 8, 11, 11, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 10, 10, 10, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 20, 20, 20, 20, 20, 20, 20, 10, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 20, 20] 20 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 41, 42, 43]) total number of confs: 39 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517170 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517170 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517170/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517170 Building REAL300004517171 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517171' /scratch/stefan/7774842/working/building/REAL300004517171 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517171 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517171/0 /scratch/stefan/7774842/working/building/REAL300004517171 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 202) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/202 `/scratch/stefan/7774842/working/3D/202' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=CC([N+](=O)[O-])=C1) `REAL300004517171.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517171 none O=C([O-])C1=CC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 8, 11, 11, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 1, 1, 11, 11, 11, 11, 11, 11, 11, 3, 1, 1, 6, 6, 6, 7, 6, 6, 6, 7, 6, 6, 1, 11, 11] 20 rigid atoms, others: [8, 9, 10, 11, 12, 13, 19, 20, 41, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43]) total number of confs: 27 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517171 none O=C([O-])C1=CC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 8, 11, 11, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 7, 7, 7, 11, 11, 11, 11, 20, 20, 20, 20, 20, 11, 11, 1, 1, 1, 1, 1, 1, 1, 7, 11, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 11, 1, 1] 20 rigid atoms, others: [1, 3, 4, 5, 6, 42, 43, 21, 22, 23, 24, 25, 26, 27] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517171 none O=C([O-])C1=CC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 8, 11, 11, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 10, 10, 10, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 20, 20, 20, 20, 20, 20, 20, 10, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 20, 20] 20 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 41, 42, 43]) total number of confs: 39 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517171 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517171 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517171/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517171 Building REAL300004517172 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517172' /scratch/stefan/7774842/working/building/REAL300004517172 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517172 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517172/0 /scratch/stefan/7774842/working/building/REAL300004517172 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 203) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/203 `/scratch/stefan/7774842/working/3D/203' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=NN(C2=CC=CC=C2)C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=C1) `REAL300004517172.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517172.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517172/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517172 none O=C([O-])C1=NN(C2=CC=CC=C2)C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 24, 24, 24, 41, 41, 41, 41, 47, 47, 47, 47, 47, 41, 41, 6, 1, 1, 1, 1, 1, 24, 41, 41, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 41, 6] 47 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 11, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 97 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517172 none O=C([O-])C1=NN(C2=CC=CC=C2)C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 46, 46, 46, 46, 47, 47, 46, 47, 47, 16, 16, 16, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 46, 47, 47, 46, 47, 47, 16, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 46] 47 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 47, 48]) total number of confs: 82 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517172 none O=C([O-])C1=NN(C2=CC=CC=C2)C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 6, 6, 1, 6, 6, 1, 1, 12, 12, 12, 23, 23, 23, 23, 46, 46, 46, 46, 46, 23, 23, 1, 6, 6, 1, 6, 6, 12, 23, 23, 46, 46, 46, 46, 46, 46, 46, 46, 46, 46, 23, 1] 47 rigid atoms, others: [1, 3, 4, 5, 6, 12, 13, 48, 28] set([0, 2, 7, 8, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 102 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517172 none O=C([O-])C1=NN(C2=CC=CC=C2)C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 41, 41, 25, 41, 41, 3, 3, 3, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 23, 41, 41, 23, 41, 41, 3, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 23] 47 rigid atoms, others: [35, 36, 47, 15, 16, 17, 18, 19, 20, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48]) total number of confs: 110 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517172 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517172 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517172/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517172 Building REAL300004517173 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517173' /scratch/stefan/7774842/working/building/REAL300004517173 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517173 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517173/0 /scratch/stefan/7774842/working/building/REAL300004517173 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 204) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/204 `/scratch/stefan/7774842/working/3D/204' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)O1) `REAL300004517173.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517173 none O=C([O-])C1=CC=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 3, 3, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 1, 1, 13, 13, 13, 3, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1] 15 rigid atoms, others: [38, 9, 10, 11, 12, 13, 14, 20, 21, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 26 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517173 none O=C([O-])C1=CC=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 8, 9, 13, 13, 13, 13, 15, 15, 15, 15, 15, 13, 13, 1, 1, 1, 9, 13, 13, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 13] 15 rigid atoms, others: [1, 3, 4, 5, 6, 7, 22, 23, 24] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517173 none O=C([O-])C1=CC=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 15, 10, 10, 10, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 15, 15, 15, 10, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7] 15 rigid atoms, others: [32, 33, 34, 35, 36, 37, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 38]) total number of confs: 28 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517173 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517173 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517173/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517173 Building REAL300004517174 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517174' /scratch/stefan/7774842/working/building/REAL300004517174 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517174 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517174/0 /scratch/stefan/7774842/working/building/REAL300004517174 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 205) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/205 `/scratch/stefan/7774842/working/3D/205' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC=C1CCC(=O)NC1=CC=C(N2CCCCC2)C=N1) `REAL300004517174.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517174/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517174 none O=C([O-])C1=CC=CC=C1CCC(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 19, 17, 13, 3, 3, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 1, 1, 19, 19, 19, 19, 17, 17, 13, 13, 3, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1] 19 rigid atoms, others: [35, 36, 13, 14, 15, 16, 17, 18, 24, 25, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 74 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517174 none O=C([O-])C1=CC=CC=C1CCC(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 12, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 5, 5, 5, 5, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19] 19 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 26, 27, 28, 29] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517174 none O=C([O-])C1=CC=CC=C1CCC(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 19, 19, 16, 5, 5, 5, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 19, 19, 19, 19, 19, 19, 16, 16, 5, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3] 19 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 47]) total number of confs: 75 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517174 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517174 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517174/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517174 Building REAL300004517175 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517175' /scratch/stefan/7774842/working/building/REAL300004517175 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517175 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517175/0 /scratch/stefan/7774842/working/building/REAL300004517175 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 206) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/206 `/scratch/stefan/7774842/working/3D/206' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=CC(C)=C1OCC(=O)[O-]) `REAL300004517175.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517175.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517175/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517175 none CC1=CC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=CC(C)=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 5, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 3, 3, 3, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 13, 13, 13, 9, 9, 24, 83, 104, 104, 13, 13, 13, 13, 3, 1, 1, 10, 10, 10, 11, 10, 10, 10, 10, 10, 10, 1, 13, 13, 13, 13, 83, 83] 123 rigid atoms, others: [33, 34, 6, 7, 8, 9, 10, 11, 45, 17, 18] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48, 49, 50, 51]) total number of confs: 377 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517175 none CC1=CC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=CC(C)=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 5, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 7, 13, 13, 13, 13, 54, 54, 54, 54, 54, 13, 13, 1, 1, 1, 1, 1, 3, 14, 21, 21, 2, 2, 2, 1, 7, 13, 13, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 13, 1, 2, 2, 2, 14, 14] 123 rigid atoms, others: [0, 1, 2, 3, 4, 46, 19, 20, 21, 22, 23, 31] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50, 51]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517175 none CC1=CC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=CC(C)=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 5, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 54, 19, 19, 19, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 54, 54, 54, 38, 40, 77, 123, 123, 123, 54, 54, 54, 54, 19, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 54, 54, 54, 54, 123, 123] 123 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 43, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 421 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517175 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517175 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517175/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517175 Building REAL300004517176 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517176' /scratch/stefan/7774842/working/building/REAL300004517176 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517176 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517176/0 /scratch/stefan/7774842/working/building/REAL300004517176 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 207) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/207 `/scratch/stefan/7774842/working/3D/207' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(CC(=O)NC2=CC=C(N3CCCCC3)C=N2)=CC=C1) `REAL300004517176.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517176 none O=C([O-])C1=CC(CC(=O)NC2=CC=C(N3CCCCC3)C=N2)=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 34, 34, 34, 9, 3, 3, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 1, 1, 34, 34, 34, 34, 9, 9, 3, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 34, 34, 34] 70 rigid atoms, others: [9, 10, 11, 12, 13, 14, 20, 21, 41, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44]) total number of confs: 72 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517176 none O=C([O-])C1=CC(CC(=O)NC2=CC=C(N3CCCCC3)C=N2)=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 6, 19, 19, 19, 34, 34, 34, 34, 70, 70, 70, 70, 70, 34, 34, 1, 1, 1, 1, 6, 6, 19, 34, 34, 70, 70, 70, 70, 70, 70, 70, 70, 70, 70, 34, 1, 1, 1] 70 rigid atoms, others: [1, 3, 4, 5, 6, 42, 43, 44, 22, 23, 24, 25] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517176 none O=C([O-])C1=CC(CC(=O)NC2=CC=C(N3CCCCC3)C=N2)=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 70, 70, 70, 32, 17, 17, 17, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 70, 70, 70, 70, 32, 32, 17, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 70, 70, 70] 70 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 41, 42, 43, 44]) total number of confs: 179 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517176 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517176 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517176/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517176 Building REAL300004517177 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517177' /scratch/stefan/7774842/working/building/REAL300004517177 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517177 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517177/0 /scratch/stefan/7774842/working/building/REAL300004517177 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 208) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/208 `/scratch/stefan/7774842/working/3D/208' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1CCCC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C1) `REAL300004517177.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517177.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517177/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517177 none O=C([O-])C1CCCC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [12, 7, 12, 7, 7, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 7, 7] 24 rigid atoms, others: [33, 34, 10, 11, 12, 13, 14, 15, 21, 22, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47]) total number of confs: 47 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517177 none O=C([O-])C1CCCC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 5, 7, 7, 7, 7, 24, 24, 24, 24, 24, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 7, 1, 1] 24 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 46, 47, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517177 none O=C([O-])C1CCCC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 24, 24, 24, 15, 15, 15, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 24, 24, 24, 24, 24, 24, 24, 24, 24, 15, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 24, 24] 24 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 45, 46, 47]) total number of confs: 65 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517177 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517177 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517177/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517177 Building REAL300004517178 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517178' /scratch/stefan/7774842/working/building/REAL300004517178 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517178 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517178/0 /scratch/stefan/7774842/working/building/REAL300004517178 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 209) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/209 `/scratch/stefan/7774842/working/3D/209' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C=N1) `REAL300004517178.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517178.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517178/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517178 none O=C([O-])C1=CC=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 3, 3, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 13, 13, 13, 13, 3, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 13] 19 rigid atoms, others: [39, 9, 10, 11, 12, 13, 14, 20, 21, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40]) total number of confs: 24 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517178 none O=C([O-])C1=CC=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 7, 7, 7, 13, 13, 13, 13, 19, 19, 19, 19, 19, 13, 13, 1, 1, 1, 1, 7, 13, 13, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 13, 1] 19 rigid atoms, others: [1, 3, 4, 5, 6, 7, 40, 22, 23, 24, 25] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517178 none O=C([O-])C1=CC=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 8, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 8, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 19, 19, 19, 19, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 19] 19 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 39, 40]) total number of confs: 36 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517178 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517178 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517178/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517178 Building REAL300004517179 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517179' /scratch/stefan/7774842/working/building/REAL300004517179 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517179 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517179/0 /scratch/stefan/7774842/working/building/REAL300004517179 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 210) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/210 `/scratch/stefan/7774842/working/3D/210' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)N=C1) `REAL300004517179.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517179.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517179/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517179 none O=C([O-])C1=CC=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)N=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 8, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 1, 1, 8, 8, 8, 8, 3, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 8] 10 rigid atoms, others: [39, 9, 10, 11, 12, 13, 14, 20, 21, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40]) total number of confs: 21 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517179 none O=C([O-])C1=CC=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)N=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 8, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 8, 8, 8, 8, 10, 10, 10, 10, 10, 8, 8, 1, 1, 1, 1, 7, 8, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 8, 1] 10 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 40, 22, 23, 24, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517179 none O=C([O-])C1=CC=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)N=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 8, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 9, 9, 9, 6, 6, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 10, 10, 10, 10, 9, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 10] 10 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 39, 40]) total number of confs: 25 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517179 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517179 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517179/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517179 Building REAL300004517180 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517180' /scratch/stefan/7774842/working/building/REAL300004517180 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517180 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517180/0 /scratch/stefan/7774842/working/building/REAL300004517180 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 211) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/211 `/scratch/stefan/7774842/working/3D/211' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CC(=O)[O-])CC(=O)NC1=CC=C(N2CCCCC2)C=N1) `REAL300004517180.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517180.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517180/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517180 none CC(C)(CC(=O)[O-])CC(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [37, 23, 37, 37, 44, 44, 44, 13, 13, 13, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 37, 37, 37, 37, 37, 37, 44, 44, 23, 23, 13, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8] 44 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 46]) total number of confs: 188 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517180 none CC(C)(CC(=O)[O-])CC(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [22, 8, 22, 22, 34, 35, 35, 3, 3, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 1, 1, 22, 22, 22, 22, 22, 22, 34, 34, 8, 8, 3, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1] 44 rigid atoms, others: [34, 35, 10, 11, 12, 13, 14, 15, 21, 22, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517180 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517180 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517180/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517180 Building REAL300004517181 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517181' /scratch/stefan/7774842/working/building/REAL300004517181 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517181 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517181/0 /scratch/stefan/7774842/working/building/REAL300004517181 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 212) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/212 `/scratch/stefan/7774842/working/3D/212' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C(F)=C1) `REAL300004517181.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517181.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517181/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517181 none O=C([O-])C1=CC=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 6, 19, 19, 3, 3, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 1, 1, 19, 19, 19, 19, 19, 3, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 19] 21 rigid atoms, others: [40, 9, 10, 11, 12, 13, 14, 20, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41]) total number of confs: 73 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517181 none O=C([O-])C1=CC=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 19, 19, 19, 19, 21, 21, 21, 21, 21, 19, 19, 1, 1, 1, 1, 1, 12, 19, 19, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 19, 1] 21 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 41, 22, 23, 24, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517181 none O=C([O-])C1=CC=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 15, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 10, 10, 10, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 21, 21, 21, 21, 21, 10, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 21] 21 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 40, 41]) total number of confs: 36 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517181 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517181 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517181/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517181 Building REAL300004517182 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517182' /scratch/stefan/7774842/working/building/REAL300004517182 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517182 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517182/0 /scratch/stefan/7774842/working/building/REAL300004517182 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 213) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/213 `/scratch/stefan/7774842/working/3D/213' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C=N1) `REAL300004517182.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517182.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517182/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517182 none O=C([O-])C1=CN=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 8, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 1, 1, 7, 7, 7, 3, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 7] 9 rigid atoms, others: [38, 9, 10, 11, 12, 13, 14, 20, 21, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39]) total number of confs: 19 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517182 none O=C([O-])C1=CN=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 8, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 6, 7, 7, 7, 7, 9, 9, 9, 9, 9, 7, 7, 1, 1, 1, 6, 7, 7, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 1] 9 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 39, 22, 23, 24] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517182 none O=C([O-])C1=CN=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 8, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 9, 9, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 9, 9, 9, 9, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 9] 9 rigid atoms, others: [32, 33, 34, 35, 36, 37, 13, 14, 15, 16, 17, 18, 19, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 38, 39]) total number of confs: 19 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517182 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517182 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517182/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517182 Building REAL300004517183 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517183' /scratch/stefan/7774842/working/building/REAL300004517183 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517183 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517183/0 /scratch/stefan/7774842/working/building/REAL300004517183 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 214) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/214 `/scratch/stefan/7774842/working/3D/214' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])[C@H]1CC[C@H](C(=O)NC2=CC=C(N3CCCCC3)C=N2)CC1) `REAL300004517183.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517183.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517183/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517183 none O=C([O-])[C@H]1CC[C@H](C(=O)NC2=CC=C(N3CCCCC3)C=N2)CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [25, 13, 25, 13, 13, 13, 13, 3, 13, 3, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 1, 1, 13, 13, 13, 13, 13, 13, 3, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 13, 13, 13, 13] 72 rigid atoms, others: [32, 43, 11, 12, 13, 14, 15, 16, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47]) total number of confs: 86 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517183 none O=C([O-])[C@H]1CC[C@H](C(=O)NC2=CC=C(N3CCCCC3)C=N2)CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 7, 13, 13, 13, 13, 72, 72, 72, 72, 72, 13, 13, 1, 1, 1, 1, 1, 1, 7, 13, 13, 72, 72, 72, 72, 72, 72, 72, 72, 72, 72, 13, 1, 1, 1, 1] 72 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 44, 45, 46, 47, 24, 25, 26, 27, 28, 29] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517183 none O=C([O-])[C@H]1CC[C@H](C(=O)NC2=CC=C(N3CCCCC3)C=N2)CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 72, 72, 72, 72, 13, 72, 13, 13, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 72, 72, 72, 72, 72, 72, 13, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 72, 72, 72, 72] 72 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 43, 44, 45, 46, 47]) total number of confs: 174 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517183 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517183 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517183/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517183 Building REAL300004517184 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517184' /scratch/stefan/7774842/working/building/REAL300004517184 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517184 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517184/0 /scratch/stefan/7774842/working/building/REAL300004517184 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 215) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/215 `/scratch/stefan/7774842/working/3D/215' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1CCC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)CC1) `REAL300004517184.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517184.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517184/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517184 none O=C([O-])C1CCC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [25, 13, 25, 13, 13, 13, 3, 3, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 3, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 13, 13, 13, 13] 72 rigid atoms, others: [32, 43, 9, 10, 11, 12, 13, 14, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47]) total number of confs: 86 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517184 none O=C([O-])C1CCC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 6, 6, 7, 13, 13, 13, 13, 72, 72, 72, 72, 72, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 72, 72, 72, 72, 72, 72, 72, 72, 72, 72, 13, 1, 1, 1, 1] 72 rigid atoms, others: [1, 3, 4, 5, 6, 7, 44, 45, 46, 47, 22, 23, 24, 25, 26, 27, 28, 29] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517184 none O=C([O-])C1CCC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 72, 72, 72, 13, 13, 13, 6, 6, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 72, 72, 72, 72, 72, 72, 72, 72, 13, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 72, 72, 72, 72] 72 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 43, 44, 45, 46, 47]) total number of confs: 179 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517184 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517184 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517184/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517184 Building REAL300004517185 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517185' /scratch/stefan/7774842/working/building/REAL300004517185 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517185 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517185/0 /scratch/stefan/7774842/working/building/REAL300004517185 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 216) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/216 `/scratch/stefan/7774842/working/3D/216' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(CC(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C1) `REAL300004517185.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517185.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517185/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517185 none O=C([O-])C1=CC=C(CC(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 9, 3, 3, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 1, 1, 17, 17, 17, 17, 9, 9, 3, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 17, 17] 43 rigid atoms, others: [10, 11, 12, 13, 14, 15, 21, 22, 42, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44]) total number of confs: 55 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517185 none O=C([O-])C1=CC=C(CC(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 5, 9, 9, 9, 17, 17, 17, 17, 44, 44, 44, 44, 44, 17, 17, 1, 1, 1, 1, 5, 5, 9, 17, 17, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 17, 1, 1] 44 rigid atoms, others: [1, 3, 4, 5, 6, 7, 43, 44, 23, 24, 25, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 93 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517185 none O=C([O-])C1=CC=C(CC(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 43, 43, 26, 16, 16, 16, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 43, 43, 43, 43, 26, 26, 16, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 43, 43] 43 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 42, 43, 44]) total number of confs: 124 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517185 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517185 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517185/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517185 Building REAL300004517186 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517186' /scratch/stefan/7774842/working/building/REAL300004517186 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517186 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517186/0 /scratch/stefan/7774842/working/building/REAL300004517186 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 217) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/217 `/scratch/stefan/7774842/working/3D/217' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN(CC(=O)NC2=CC=C(N3CCCCC3)C=N2)N=N1) `REAL300004517186.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517186.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517186/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517186 none O=C([O-])C1=CN(CC(=O)NC2=CC=C(N3CCCCC3)C=N2)N=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [110, 110, 110, 110, 110, 21, 3, 3, 3, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 1, 1, 110, 110, 110, 21, 21, 3, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1] 158 rigid atoms, others: [40, 9, 10, 11, 12, 13, 14, 20, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 187 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517186 none O=C([O-])C1=CN(CC(=O)NC2=CC=C(N3CCCCC3)C=N2)N=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 9, 64, 64, 64, 110, 110, 110, 110, 158, 158, 158, 158, 158, 110, 110, 1, 1, 1, 9, 9, 64, 110, 110, 158, 158, 158, 158, 158, 158, 158, 158, 158, 158, 110] 158 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 22, 23, 24] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 331 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517186 none O=C([O-])C1=CN(CC(=O)NC2=CC=C(N3CCCCC3)C=N2)N=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 158 conformations in input total number of sets (complete confs): 158 using faster count positions algorithm for large data unique positions, atoms: [158, 158, 158, 158, 158, 91, 21, 21, 21, 10, 10, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 158, 158, 158, 91, 91, 21, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11] 158 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 40]) total number of confs: 432 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517186 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517186 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517186/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517186 Building REAL300004517187 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517187' /scratch/stefan/7774842/working/building/REAL300004517187 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517187 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517187/0 /scratch/stefan/7774842/working/building/REAL300004517187 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 218) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/218 `/scratch/stefan/7774842/working/3D/218' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=CC=C1C(=O)[O-]) `REAL300004517187.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517187.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517187/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517187 none CC1=NC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 3, 3, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 1, 1, 9, 9, 9, 9, 15, 15, 9, 9, 9, 3, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 9, 9] 15 rigid atoms, others: [6, 7, 8, 9, 10, 11, 17, 18, 41, 29, 30] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43]) total number of confs: 46 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517187 none CC1=NC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 6, 9, 9, 9, 9, 15, 15, 15, 15, 15, 9, 9, 1, 1, 1, 1, 3, 3, 2, 2, 2, 6, 9, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 9, 1, 1] 15 rigid atoms, others: [0, 1, 2, 3, 4, 42, 43, 19, 20, 21, 22] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517187 none CC1=NC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 13, 13, 13, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 13, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 15, 15] 15 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 10, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 41, 42, 43]) total number of confs: 35 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517187 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517187 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517187/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517187 Building REAL300004517188 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517188' /scratch/stefan/7774842/working/building/REAL300004517188 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517188 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517188/0 /scratch/stefan/7774842/working/building/REAL300004517188 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 219) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/219 `/scratch/stefan/7774842/working/3D/219' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C1) `REAL300004517188.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517188.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517188/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517188 none O=C([O-])C1=CC=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 7, 3, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 3, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 7, 7] 10 rigid atoms, others: [39, 9, 10, 11, 12, 13, 14, 20, 21, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41]) total number of confs: 38 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517188 none O=C([O-])C1=CC=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 7, 10, 10, 10, 10, 10, 7, 7, 1, 1, 1, 1, 4, 7, 7, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 7, 1, 1] 10 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 40, 41, 22, 23, 24, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517188 none O=C([O-])C1=CC=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [10, 8, 10, 9, 10, 10, 8, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 10, 10, 10, 10, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 10, 10] 10 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 39, 40, 41]) total number of confs: 34 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517188 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517188 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517188/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517188 Building REAL300004517189 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517189' /scratch/stefan/7774842/working/building/REAL300004517189 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517189 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517189/0 /scratch/stefan/7774842/working/building/REAL300004517189 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 220) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/220 `/scratch/stefan/7774842/working/3D/220' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])[C@@H]1CC[C@H](C(=O)NC2=CC=C(N3CCCCC3)C=N2)C1) `REAL300004517189.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517189.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517189/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517189 none O=C([O-])[C@@H]1CC[C@H](C(=O)NC2=CC=C(N3CCCCC3)C=N2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [34, 20, 34, 20, 20, 20, 20, 3, 20, 3, 3, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 1, 1, 20, 20, 20, 20, 20, 3, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 20, 20] 47 rigid atoms, others: [42, 11, 12, 13, 14, 15, 16, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44]) total number of confs: 112 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517189 none O=C([O-])[C@@H]1CC[C@H](C(=O)NC2=CC=C(N3CCCCC3)C=N2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 20, 20, 20, 20, 47, 47, 47, 47, 47, 20, 20, 1, 1, 1, 1, 1, 11, 20, 20, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 20, 1, 1] 47 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 43, 44, 24, 25, 26, 27, 28] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 88 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517189 none O=C([O-])[C@@H]1CC[C@H](C(=O)NC2=CC=C(N3CCCCC3)C=N2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 47, 47, 47, 14, 47, 14, 14, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 47, 47, 47, 47, 47, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 47, 47] 47 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 42, 43, 44]) total number of confs: 108 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517189 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517189 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517189/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517189 Building REAL300004517190 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517190' /scratch/stefan/7774842/working/building/REAL300004517190 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517190 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517190/0 /scratch/stefan/7774842/working/building/REAL300004517190 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 221) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/221 `/scratch/stefan/7774842/working/3D/221' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=CC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=C1) `REAL300004517190.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517190.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517190/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517190 none O=C([O-])CC1=CC=CC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [40, 20, 40, 12, 12, 12, 12, 12, 3, 3, 3, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 12, 20, 20, 12, 12, 12, 3, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 12] 59 rigid atoms, others: [32, 43, 11, 12, 13, 14, 15, 16, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44]) total number of confs: 148 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517190 none O=C([O-])CC1=CC=CC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [7, 2, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 12, 12, 12, 12, 45, 45, 45, 45, 45, 12, 12, 1, 2, 2, 1, 1, 1, 7, 12, 12, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 12, 1] 59 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 44, 24, 27, 28, 29] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 86 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517190 none O=C([O-])CC1=CC=CC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 45, 45, 45, 45, 45, 17, 17, 17, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 45, 59, 59, 45, 45, 45, 17, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 45] 59 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 43, 44]) total number of confs: 165 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517190 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517190 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517190/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517190 Building REAL300004517191 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517191' /scratch/stefan/7774842/working/building/REAL300004517191 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517191 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517191/0 /scratch/stefan/7774842/working/building/REAL300004517191 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 222) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/222 `/scratch/stefan/7774842/working/3D/222' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C=CO1) `REAL300004517191.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517191 none O=C([O-])CC1=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C=CO1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [21, 15, 21, 13, 13, 3, 3, 3, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 13, 13, 13, 15, 15, 3, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 13, 13] 25 rigid atoms, others: [39, 8, 9, 10, 11, 12, 13, 19, 20, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41]) total number of confs: 63 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517191 none O=C([O-])CC1=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C=CO1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [7, 2, 7, 1, 1, 1, 1, 9, 9, 9, 13, 13, 13, 13, 23, 23, 23, 23, 23, 13, 13, 1, 1, 1, 2, 2, 9, 13, 13, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 13, 1, 1] 25 rigid atoms, others: [3, 4, 5, 6, 40, 41, 21, 22, 23] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517191 none O=C([O-])CC1=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C=CO1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 12, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 23, 23, 14, 14, 14, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 23, 23, 23, 25, 25, 14, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 23, 23] 25 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 39, 40, 41]) total number of confs: 53 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517191 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517191 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517191/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517191 Building REAL300004517192 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517192' /scratch/stefan/7774842/working/building/REAL300004517192 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517192 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517192/0 /scratch/stefan/7774842/working/building/REAL300004517192 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 223) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/223 `/scratch/stefan/7774842/working/3D/223' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=COC(CC(=O)[O-])=C1C(=O)NC1=CC=C(N2CCCCC2)C=N1) `REAL300004517192.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517192.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517192/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517192 none CC1=COC(CC(=O)[O-])=C1C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 5, 1, 11, 11, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 13, 18, 18, 3, 3, 3, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 11, 11, 11, 11, 13, 13, 3, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1] 22 rigid atoms, others: [32, 33, 44, 12, 13, 14, 15, 16, 17, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 59 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517192 none CC1=COC(CC(=O)[O-])=C1C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 5, 1, 11, 11, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 6, 6, 1, 1, 7, 7, 7, 11, 11, 11, 11, 20, 20, 20, 20, 20, 11, 11, 2, 2, 2, 1, 2, 2, 7, 11, 11, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 11] 22 rigid atoms, others: [0, 1, 2, 3, 4, 5, 9, 10, 28] set([6, 7, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517192 none CC1=COC(CC(=O)[O-])=C1C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 5, 1, 11, 11, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 22, 22, 22, 14, 14, 14, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 20, 20, 20, 20, 22, 22, 14, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10] 22 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 44]) total number of confs: 49 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517192 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517192 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517192/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517192 Building REAL300004517193 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517193' /scratch/stefan/7774842/working/building/REAL300004517193 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517193 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517193/0 /scratch/stefan/7774842/working/building/REAL300004517193 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 224) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/224 `/scratch/stefan/7774842/working/3D/224' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=NC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=C1) `REAL300004517193.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517193.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517193/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517193 none O=C([O-])C1=CC=NC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 1, 1, 18, 18, 18, 3, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 18] 21 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 21, 22, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40]) total number of confs: 32 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517193 none O=C([O-])C1=CC=NC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 18, 18, 18, 18, 21, 21, 21, 21, 21, 18, 18, 1, 1, 1, 12, 18, 18, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 18, 1] 21 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 40, 23, 24, 25] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517193 none O=C([O-])C1=CC=NC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 11, 11, 11, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 21, 21, 21, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 21] 21 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 39, 40]) total number of confs: 36 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517193 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517193 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517193/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517193 Building REAL300004517194 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517194' /scratch/stefan/7774842/working/building/REAL300004517194 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517194 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517194/0 /scratch/stefan/7774842/working/building/REAL300004517194 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 225) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/225 `/scratch/stefan/7774842/working/3D/225' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C12CC(C(=O)NC3=CC=C(N4CCCCC4)C=N3)(C1)C2) `REAL300004517194.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517194.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517194/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517194 none O=C([O-])C12CC(C(=O)NC3=CC=C(N4CCCCC4)C=N3)(C1)C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 8, 15, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 8, 8, 8, 8, 3, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 8, 8, 8, 8] 15 rigid atoms, others: [38, 8, 9, 10, 11, 12, 13, 19, 20, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42]) total number of confs: 52 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517194 none O=C([O-])C12CC(C(=O)NC3=CC=C(N4CCCCC4)C=N3)(C1)C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 6, 6, 6, 8, 8, 8, 8, 15, 15, 15, 15, 15, 8, 8, 1, 1, 1, 1, 6, 8, 8, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 1, 1, 1, 1] 15 rigid atoms, others: [1, 3, 4, 5, 6, 39, 40, 41, 42, 21, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517194 none O=C([O-])C12CC(C(=O)NC3=CC=C(N4CCCCC4)C=N3)(C1)C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 15, 15, 15, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 15, 15, 15, 15, 15, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 15, 15, 15, 15] 15 rigid atoms, others: [32, 33, 34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 38, 39, 40, 41, 42]) total number of confs: 31 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517194 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517194 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517194/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517194 Building REAL300004517195 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517195' /scratch/stefan/7774842/working/building/REAL300004517195 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517195 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517195/0 /scratch/stefan/7774842/working/building/REAL300004517195 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 226) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/226 `/scratch/stefan/7774842/working/3D/226' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1(C(=O)NC2=CC=C(N3CCCCC3)C=N2)CCC1) `REAL300004517195.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517195.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517195/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517195 none O=C([O-])C1(C(=O)NC2=CC=C(N3CCCCC3)C=N2)CCC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [15, 9, 15, 3, 3, 3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 1, 1, 9, 9, 9, 3, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 9, 9, 9, 9, 9, 9] 30 rigid atoms, others: [35, 6, 7, 8, 9, 10, 11, 17, 18, 23, 24] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41]) total number of confs: 56 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517195 none O=C([O-])C1(C(=O)NC2=CC=C(N3CCCCC3)C=N2)CCC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 6, 6, 6, 9, 9, 9, 9, 30, 30, 30, 30, 30, 9, 9, 1, 1, 1, 6, 9, 9, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 9, 1, 1, 1, 1, 1, 1] 30 rigid atoms, others: [1, 3, 4, 37, 38, 39, 40, 41, 19, 20, 21, 36] set([0, 2, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517195 none O=C([O-])C1(C(=O)NC2=CC=C(N3CCCCC3)C=N2)CCC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 14, 14, 14, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 9, 9, 30, 30, 30, 14, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 30, 30, 30, 30, 30, 30] 30 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 82 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517195 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517195 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517195/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517195 Building REAL300004517196 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517196' /scratch/stefan/7774842/working/building/REAL300004517196 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517196 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517196/0 /scratch/stefan/7774842/working/building/REAL300004517196 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 227) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/227 `/scratch/stefan/7774842/working/3D/227' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1CCC(CC(=O)NC2=CC=C(N3CCCCC3)C=N2)CC1) `REAL300004517196.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517196.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517196/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517196 none O=C([O-])C1CCC(CC(=O)NC2=CC=C(N3CCCCC3)C=N2)CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 176 conformations in input total number of sets (complete confs): 176 using faster count positions algorithm for large data unique positions, atoms: [139, 77, 139, 77, 77, 74, 25, 3, 3, 3, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 74, 77, 77, 77, 77, 77, 77, 77, 25, 25, 3, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 77, 77, 77, 77] 176 rigid atoms, others: [34, 35, 10, 11, 12, 13, 14, 15, 21, 22, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49, 50]) total number of confs: 507 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517196 none O=C([O-])C1CCC(CC(=O)NC2=CC=C(N3CCCCC3)C=N2)CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 176 conformations in input total number of sets (complete confs): 176 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 10, 44, 44, 44, 77, 77, 77, 77, 176, 176, 176, 176, 176, 77, 77, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 44, 77, 77, 176, 176, 176, 176, 176, 176, 176, 176, 176, 176, 77, 1, 1, 1, 1] 176 rigid atoms, others: [1, 3, 4, 5, 6, 7, 47, 48, 49, 50, 23, 24, 25, 26, 27, 28, 29, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 352 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517196 none O=C([O-])C1CCC(CC(=O)NC2=CC=C(N3CCCCC3)C=N2)CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 176 conformations in input total number of sets (complete confs): 176 using faster count positions algorithm for large data unique positions, atoms: [176, 176, 176, 176, 176, 169, 117, 18, 18, 18, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 169, 176, 176, 176, 176, 176, 176, 176, 117, 117, 18, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 176, 176, 176, 176] 176 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 46, 47, 48, 49, 50]) total number of confs: 638 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517196 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517196 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517196/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517196 Building REAL300004517197 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517197' /scratch/stefan/7774842/working/building/REAL300004517197 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517197 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517197/0 /scratch/stefan/7774842/working/building/REAL300004517197 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 228) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/228 `/scratch/stefan/7774842/working/3D/228' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C12CCC(C(=O)NC3=CC=C(N4CCCCC4)C=N3)(CC1)C2) `REAL300004517197.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517197/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517197 none O=C([O-])C12CCC(C(=O)NC3=CC=C(N4CCCCC4)C=N3)(CC1)C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [25, 13, 25, 13, 13, 13, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 1, 1, 13, 13, 13, 13, 13, 13, 13, 3, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 13, 13, 13, 13, 13, 13] 59 rigid atoms, others: [9, 10, 11, 12, 13, 14, 20, 21, 42, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48]) total number of confs: 73 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517197 none O=C([O-])C12CCC(C(=O)NC3=CC=C(N4CCCCC4)C=N3)(CC1)C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 7, 7, 7, 13, 13, 13, 13, 59, 59, 59, 59, 59, 13, 13, 1, 1, 1, 1, 1, 1, 1, 7, 13, 13, 59, 59, 59, 59, 59, 59, 59, 59, 59, 59, 13, 1, 1, 1, 1, 1, 1] 59 rigid atoms, others: [1, 3, 4, 5, 6, 7, 43, 44, 45, 46, 47, 48, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517197 none O=C([O-])C12CCC(C(=O)NC3=CC=C(N4CCCCC4)C=N3)(CC1)C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 59, 59, 59, 13, 13, 13, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 59, 59, 59, 59, 59, 59, 59, 13, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 59, 59, 59, 59, 59, 59] 59 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 91 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517197 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517197 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517197/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517197 Building REAL300004517198 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517198' /scratch/stefan/7774842/working/building/REAL300004517198 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517198 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517198/0 /scratch/stefan/7774842/working/building/REAL300004517198 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 229) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/229 `/scratch/stefan/7774842/working/3D/229' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C12CCC(C(=O)NC3=CC=C(N4CCCCC4)C=N3)(CC1)CC2) `REAL300004517198.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517198/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517198 none O=C([O-])C12CCC(C(=O)NC3=CC=C(N4CCCCC4)C=N3)(CC1)CC2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [9, 3, 9, 3, 9, 9, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 3, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 9, 9, 9, 9, 9, 9, 9, 9] 24 rigid atoms, others: [32, 43, 9, 10, 11, 12, 13, 14, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 55 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517198 none O=C([O-])C12CCC(C(=O)NC3=CC=C(N4CCCCC4)C=N3)(CC1)CC2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 6, 6, 7, 9, 9, 9, 9, 24, 24, 24, 24, 24, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 7, 9, 9, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 9, 1, 1, 1, 1, 1, 1, 1, 1] 24 rigid atoms, others: [1, 3, 4, 5, 6, 7, 22, 23, 24, 25, 26, 27, 28, 29, 44, 45, 46, 47, 48, 49, 50, 51] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517198 none O=C([O-])C12CCC(C(=O)NC3=CC=C(N4CCCCC4)C=N3)(CC1)CC2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [24, 13, 24, 13, 24, 24, 13, 13, 13, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 24, 24, 24, 13, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 24, 24, 24, 24, 24, 24, 24, 24] 24 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 154 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517198 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517198 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517198/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517198 Building REAL300004517199 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517199' /scratch/stefan/7774842/working/building/REAL300004517199 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517199 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517199/0 /scratch/stefan/7774842/working/building/REAL300004517199 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 230) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/230 `/scratch/stefan/7774842/working/3D/230' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CC(=O)[O-])CC(=O)NC1=CC=C(N2CCCCC2)C=N1) `REAL300004517199.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517199.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517199/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517199 none CC(C)(CC(=O)[O-])CC(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [37, 23, 37, 37, 44, 44, 44, 13, 13, 13, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 37, 37, 37, 37, 37, 37, 44, 44, 23, 23, 13, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8] 44 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 46]) total number of confs: 188 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517199 none CC(C)(CC(=O)[O-])CC(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [22, 8, 22, 22, 34, 35, 35, 3, 3, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 1, 1, 22, 22, 22, 22, 22, 22, 34, 34, 8, 8, 3, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1] 44 rigid atoms, others: [34, 35, 10, 11, 12, 13, 14, 15, 21, 22, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517199 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517199 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517199/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517199 Building REAL300004517200 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517200' /scratch/stefan/7774842/working/building/REAL300004517200 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517200 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517200/0 /scratch/stefan/7774842/working/building/REAL300004517200 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 231) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/231 `/scratch/stefan/7774842/working/3D/231' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(=O)[O-])CC(=O)NC1=CC=C(N2CCCCC2)C=N1) `REAL300004517200.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517200.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517200/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517200 none CC(CC(=O)[O-])CC(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 11, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [108, 72, 108, 135, 135, 135, 21, 21, 21, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 110, 110, 110, 110, 135, 135, 72, 72, 21, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10] 135 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 43]) total number of confs: 624 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517200 none CC(CC(=O)[O-])CC(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 11, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [45, 21, 44, 98, 112, 112, 3, 3, 3, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 47, 47, 47, 47, 98, 98, 21, 21, 3, 1, 1, 10, 10, 10, 10, 10, 10, 10, 11, 10, 10, 1] 135 rigid atoms, others: [32, 43, 9, 10, 11, 12, 13, 14, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 509 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517200 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517200 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517200/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517200 Building REAL300004517201 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517201' /scratch/stefan/7774842/working/building/REAL300004517201 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517201 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517201/0 /scratch/stefan/7774842/working/building/REAL300004517201 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 232) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/232 `/scratch/stefan/7774842/working/3D/232' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C2N=CC=C(C(=O)NC3=CC=C(N4CCCCC4)C=N3)N2N=C1) `REAL300004517201.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517201.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517201/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517201 none O=C([O-])C1=C2N=CC=C(C(=O)NC3=CC=C(N4CCCCC4)C=N3)N2N=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 8, 8, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [13, 11, 13, 11, 11, 11, 11, 11, 3, 3, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 1, 1, 11, 11, 11, 11, 11, 3, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 11] 19 rigid atoms, others: [42, 11, 12, 13, 14, 15, 16, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43]) total number of confs: 33 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517201 none O=C([O-])C1=C2N=CC=C(C(=O)NC3=CC=C(N4CCCCC4)C=N3)N2N=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 8, 8, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 8, 11, 11, 11, 11, 19, 19, 19, 19, 19, 11, 11, 1, 1, 1, 1, 1, 8, 11, 11, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 11, 1] 19 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 43, 24, 25, 26, 27, 28] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517201 none O=C([O-])C1=C2N=CC=C(C(=O)NC3=CC=C(N4CCCCC4)C=N3)N2N=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 8, 8, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 19, 13, 13, 13, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 19, 19, 19, 19, 19, 13, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 19] 19 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 42, 43]) total number of confs: 37 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517201 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517201 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517201/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517201 Building REAL300004517202 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517202' /scratch/stefan/7774842/working/building/REAL300004517202 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517202 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517202/0 /scratch/stefan/7774842/working/building/REAL300004517202 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 233) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/233 `/scratch/stefan/7774842/working/3D/233' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)NC2=CC=CC=C21) `REAL300004517202.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517202.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517202/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517202 none O=C([O-])CC1=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)NC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [16, 14, 16, 12, 12, 3, 3, 3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 1, 1, 12, 12, 12, 12, 12, 12, 12, 14, 14, 3, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 12, 12, 12, 12, 12] 21 rigid atoms, others: [32, 43, 8, 9, 10, 11, 12, 13, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48]) total number of confs: 47 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517202 none O=C([O-])CC1=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)NC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 1, 1, 1, 1, 8, 8, 8, 12, 12, 12, 12, 19, 19, 19, 19, 19, 12, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 12, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 12, 1, 1, 1, 1, 1] 21 rigid atoms, others: [3, 4, 5, 6, 44, 45, 46, 47, 48, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517202 none O=C([O-])CC1=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)NC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 19, 19, 14, 14, 14, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 9, 9, 19, 19, 19, 19, 19, 19, 19, 21, 21, 14, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 19, 19, 19, 19, 19] 21 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 43, 44, 45, 46, 47, 48]) total number of confs: 51 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517202 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517202 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517202/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517202 Building REAL300004517203 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517203' /scratch/stefan/7774842/working/building/REAL300004517203 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517203 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517203/0 /scratch/stefan/7774842/working/building/REAL300004517203 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 234) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/234 `/scratch/stefan/7774842/working/3D/234' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=NO1) `REAL300004517203.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517203/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517203 none O=C([O-])C1=CC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=NO1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 8, 12, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 3, 3, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 1, 1, 14, 14, 14, 3, 1, 1, 7, 7, 7, 8, 7, 7, 7, 8, 7, 7, 1] 17 rigid atoms, others: [37, 8, 9, 10, 11, 12, 13, 19, 20, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 31 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517203 none O=C([O-])C1=CC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=NO1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 8, 12, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 8, 8, 9, 14, 14, 14, 14, 17, 17, 17, 17, 17, 14, 14, 1, 1, 1, 9, 14, 14, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 14] 17 rigid atoms, others: [1, 3, 4, 5, 6, 21, 22, 23] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517203 none O=C([O-])C1=CC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=NO1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 8, 12, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 10, 10, 10, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 17, 17, 17, 10, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7] 17 rigid atoms, others: [32, 33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 37]) total number of confs: 31 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517203 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517203 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517203/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517203 Building REAL300004517204 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517204' /scratch/stefan/7774842/working/building/REAL300004517204 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517204 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517204/0 /scratch/stefan/7774842/working/building/REAL300004517204 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 235) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/235 `/scratch/stefan/7774842/working/3D/235' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1(C(=O)NC2=CC=C(N3CCCCC3)C=N2)CCCC1) `REAL300004517204.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517204.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517204/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517204 none O=C([O-])C1(C(=O)NC2=CC=C(N3CCCCC3)C=N2)CCCC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [13, 7, 13, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 1, 1, 7, 7, 7, 7, 3, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 7, 7, 7, 7, 7, 7, 7, 7] 33 rigid atoms, others: [36, 6, 7, 8, 9, 10, 11, 17, 18, 24, 25] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 49 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517204 none O=C([O-])C1(C(=O)NC2=CC=C(N3CCCCC3)C=N2)CCCC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 4, 4, 4, 7, 7, 7, 7, 33, 33, 33, 33, 33, 7, 7, 1, 1, 1, 1, 4, 7, 7, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 7, 1, 1, 1, 1, 1, 1, 1, 1] 33 rigid atoms, others: [1, 3, 4, 37, 38, 39, 40, 41, 42, 43, 44, 19, 20, 21, 22] set([0, 2, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517204 none O=C([O-])C1(C(=O)NC2=CC=C(N3CCCCC3)C=N2)CCCC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 13, 13, 13, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 33, 33, 33, 33, 13, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 33, 33, 33, 33, 33, 33, 33, 33] 33 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 97 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517204 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517204 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517204/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517204 Building REAL300004517205 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517205' /scratch/stefan/7774842/working/building/REAL300004517205 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517205 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517205/0 /scratch/stefan/7774842/working/building/REAL300004517205 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 236) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/236 `/scratch/stefan/7774842/working/3D/236' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C2CCCC(CC(=O)NC3=CC=C(N4CCCCC4)C=N3)C2=C1) `REAL300004517205.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517205.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517205/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517205 none O=C([O-])C1=CC=C2CCCC(CC(=O)NC3=CC=C(N4CCCCC4)C=N3)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 20, 3, 3, 3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 1, 1, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 20, 20, 3, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 44] 61 rigid atoms, others: [41, 42, 14, 15, 16, 17, 18, 19, 53, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 54]) total number of confs: 149 number of broken/clashed sets: 22 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517205 none O=C([O-])C1=CC=C2CCCC(CC(=O)NC3=CC=C(N4CCCCC4)C=N3)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 25, 25, 25, 44, 44, 44, 44, 61, 61, 61, 61, 61, 44, 44, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 25, 44, 44, 61, 61, 61, 61, 61, 61, 61, 61, 61, 61, 44, 1] 61 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 54] set([0, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 142 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517205 none O=C([O-])C1=CC=C2CCCC(CC(=O)NC3=CC=C(N4CCCCC4)C=N3)C2=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 61, 61, 61, 61, 61, 61, 61, 61, 52, 16, 16, 16, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 9, 9, 61, 61, 61, 61, 61, 61, 61, 61, 61, 61, 61, 52, 52, 16, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 61] 61 rigid atoms, others: [51, 50, 43, 44, 45, 46, 47, 48, 49, 18, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 53, 54]) total number of confs: 212 number of broken/clashed sets: 22 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517205 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517205 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517205/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517205 Building REAL300004517206 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517206' /scratch/stefan/7774842/working/building/REAL300004517206 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517206 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517206/0 /scratch/stefan/7774842/working/building/REAL300004517206 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 237) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/237 `/scratch/stefan/7774842/working/3D/237' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C(C(=O)[O-])O1) `REAL300004517206.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517206.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517206/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517206 none CC1=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 1, 11, 11, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 3, 3, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 3, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 14] 23 rigid atoms, others: [5, 6, 7, 8, 9, 10, 16, 17, 40, 28, 29] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41]) total number of confs: 27 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517206 none CC1=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 1, 11, 11, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 8, 8, 9, 14, 14, 14, 14, 23, 23, 23, 23, 23, 14, 14, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 14, 14, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 14, 1] 23 rigid atoms, others: [0, 1, 2, 3, 41, 18, 19, 20, 21, 22, 23] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517206 none CC1=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 1, 11, 11, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 11, 11, 11, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 23, 23, 23, 23, 23, 23, 23, 23, 23, 11, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 23] 23 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 40, 41]) total number of confs: 42 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517206 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517206 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517206/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517206 Building REAL300004517207 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517207' /scratch/stefan/7774842/working/building/REAL300004517207 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517207 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517207/0 /scratch/stefan/7774842/working/building/REAL300004517207 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 238) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/238 `/scratch/stefan/7774842/working/3D/238' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])OC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=C1) `REAL300004517207.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517207.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517207/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517207 none CC1=C(C(=O)[O-])OC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 19, 19, 13, 3, 3, 3, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 13, 13, 13, 13, 3, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 13] 23 rigid atoms, others: [40, 10, 11, 12, 13, 14, 15, 21, 22, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41]) total number of confs: 53 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517207 none CC1=C(C(=O)[O-])OC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 9, 9, 9, 13, 13, 13, 13, 23, 23, 23, 23, 23, 13, 13, 1, 2, 2, 2, 9, 13, 13, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 13, 1] 23 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 41, 23] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 53 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517207 none CC1=C(C(=O)[O-])OC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 16, 16, 16, 9, 9, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 23, 23, 23, 23, 16, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 23] 23 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 40, 41]) total number of confs: 54 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517207 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517207 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517207/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517207 Building REAL300004517208 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517208' /scratch/stefan/7774842/working/building/REAL300004517208 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517208 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517208/0 /scratch/stefan/7774842/working/building/REAL300004517208 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 239) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/239 `/scratch/stefan/7774842/working/3D/239' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN(CC(=O)NC2=CC=C(N3CCCCC3)C=N2)N=C1) `REAL300004517208.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517208.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517208/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517208 none O=C([O-])C1=CN(CC(=O)NC2=CC=C(N3CCCCC3)C=N2)N=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [98, 98, 98, 98, 98, 22, 3, 3, 3, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 1, 1, 98, 98, 98, 22, 22, 3, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 98] 142 rigid atoms, others: [40, 9, 10, 11, 12, 13, 14, 20, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41]) total number of confs: 176 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517208 none O=C([O-])C1=CN(CC(=O)NC2=CC=C(N3CCCCC3)C=N2)N=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 9, 58, 58, 58, 98, 98, 98, 98, 142, 142, 142, 142, 142, 98, 98, 1, 1, 1, 9, 9, 58, 98, 98, 142, 142, 142, 142, 142, 142, 142, 142, 142, 142, 98, 1] 142 rigid atoms, others: [1, 3, 4, 5, 6, 41, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 305 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517208 none O=C([O-])C1=CN(CC(=O)NC2=CC=C(N3CCCCC3)C=N2)N=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 142 conformations in input total number of sets (complete confs): 142 using faster count positions algorithm for large data unique positions, atoms: [142, 142, 142, 142, 142, 90, 21, 21, 21, 10, 10, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 142, 142, 142, 90, 90, 21, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 142] 142 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 40, 41]) total number of confs: 406 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517208 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517208 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517208/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517208 Building REAL300004517209 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517209' /scratch/stefan/7774842/working/building/REAL300004517209 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517209 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517209/0 /scratch/stefan/7774842/working/building/REAL300004517209 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 240) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/240 `/scratch/stefan/7774842/working/3D/240' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=CC1=CC=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)O1) `REAL300004517209.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517209.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517209/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517209 none O=C([O-])C=CC1=CC=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [53, 44, 53, 44, 15, 15, 15, 15, 3, 3, 3, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 15, 44, 44, 15, 15, 3, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1] 59 rigid atoms, others: [42, 11, 12, 13, 14, 15, 16, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 141 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517209 none O=C([O-])C=CC1=CC=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [23, 11, 24, 11, 1, 1, 1, 1, 1, 1, 9, 9, 10, 15, 15, 15, 15, 40, 40, 40, 40, 40, 15, 15, 1, 11, 11, 1, 1, 10, 15, 15, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 15] 59 rigid atoms, others: [4, 5, 6, 7, 8, 9, 24, 27, 28] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517209 none O=C([O-])C=CC1=CC=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 59, 40, 40, 40, 40, 20, 20, 20, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 40, 59, 59, 40, 40, 20, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10] 59 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 42]) total number of confs: 145 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517209 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517209 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517209/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517209 Building REAL300004517210 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517210' /scratch/stefan/7774842/working/building/REAL300004517210 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517210 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517210/0 /scratch/stefan/7774842/working/building/REAL300004517210 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 241) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/241 `/scratch/stefan/7774842/working/3D/241' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1(C(=O)NC2=CC=C(N3CCCCC3)C=N2)CC2(CCC2)C1) `REAL300004517210.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517210.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517210/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517210 none O=C([O-])C1(C(=O)NC2=CC=C(N3CCCCC3)C=N2)CC2(CCC2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [14, 8, 14, 3, 3, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 1, 1, 8, 8, 8, 8, 8, 8, 3, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 26 rigid atoms, others: [38, 6, 7, 8, 9, 10, 11, 17, 18, 26, 27] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 52 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517210 none O=C([O-])C1(C(=O)NC2=CC=C(N3CCCCC3)C=N2)CC2(CCC2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 5, 5, 5, 8, 8, 8, 8, 26, 26, 26, 26, 26, 8, 8, 1, 1, 1, 1, 1, 1, 5, 8, 8, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 26 rigid atoms, others: [1, 3, 4, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 20, 21, 22, 23, 24] set([0, 2, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517210 none O=C([O-])C1(C(=O)NC2=CC=C(N3CCCCC3)C=N2)CC2(CCC2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 13, 13, 13, 6, 6, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 26, 26, 26, 26, 26, 26, 13, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26] 26 rigid atoms, others: [32, 33, 34, 35, 36, 37, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 77 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517210 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517210 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517210/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517210 Building REAL300004517211 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517211' /scratch/stefan/7774842/working/building/REAL300004517211 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517211 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517211/0 /scratch/stefan/7774842/working/building/REAL300004517211 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 242) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/242 `/scratch/stefan/7774842/working/3D/242' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C1) `REAL300004517211.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517211 none O=C([O-])COC1=CC=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 169 conformations in input total number of sets (complete confs): 169 using faster count positions algorithm for large data unique positions, atoms: [150, 107, 150, 32, 13, 9, 13, 13, 3, 3, 3, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 13, 13, 107, 107, 13, 13, 3, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 13, 13] 169 rigid atoms, others: [32, 43, 11, 12, 13, 14, 15, 16, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45]) total number of confs: 521 number of broken/clashed sets: 35 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517211 none O=C([O-])COC1=CC=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 169 conformations in input total number of sets (complete confs): 169 using faster count positions algorithm for large data unique positions, atoms: [36, 17, 36, 4, 1, 1, 1, 1, 1, 1, 7, 7, 7, 13, 13, 13, 13, 69, 69, 69, 69, 69, 13, 13, 1, 1, 17, 17, 1, 1, 7, 13, 13, 69, 69, 69, 69, 69, 69, 69, 69, 69, 69, 13, 1, 1] 169 rigid atoms, others: [4, 5, 6, 7, 8, 9, 44, 45, 24, 25, 28, 29] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 206 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517211 none O=C([O-])COC1=CC=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 169 conformations in input total number of sets (complete confs): 169 using faster count positions algorithm for large data unique positions, atoms: [169, 169, 169, 108, 69, 46, 69, 69, 21, 21, 21, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 69, 69, 169, 169, 69, 69, 21, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 69, 69] 169 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 43, 44, 45]) total number of confs: 613 number of broken/clashed sets: 35 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517211 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517211 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517211/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517211 Building REAL300004517212 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517212' /scratch/stefan/7774842/working/building/REAL300004517212 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517212 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517212/0 /scratch/stefan/7774842/working/building/REAL300004517212 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 243) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/243 `/scratch/stefan/7774842/working/3D/243' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=NN(C2=CC=CC=C2)C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C1) `REAL300004517212.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517212 none O=C([O-])C1=NN(C2=CC=CC=C2)C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [9, 4, 9, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 8, 8, 8, 13, 13, 13, 13, 19, 19, 19, 19, 19, 13, 13, 4, 1, 1, 1, 1, 1, 4, 8, 13, 13, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 13, 4, 4] 19 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 11, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 51 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517212 none O=C([O-])C1=NN(C2=CC=CC=C2)C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 18, 19, 18, 18, 18, 18, 19, 19, 18, 19, 19, 11, 11, 11, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 18, 19, 19, 19, 19, 19, 18, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 18, 18] 19 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49, 50]) total number of confs: 56 number of broken/clashed sets: 0 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517212 none O=C([O-])C1=NN(C2=CC=CC=C2)C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [7, 1, 7, 1, 1, 1, 1, 4, 4, 1, 4, 4, 1, 1, 5, 5, 5, 8, 8, 8, 8, 18, 18, 18, 18, 18, 8, 8, 1, 4, 4, 1, 4, 4, 1, 5, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 8, 1, 1] 19 rigid atoms, others: [1, 34, 3, 4, 5, 6, 12, 13, 49, 50, 28] set([0, 2, 7, 8, 9, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517212 none O=C([O-])C1=NN(C2=CC=CC=C2)C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 1, 1, 1, 1, 1, 1, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [16, 8, 16, 8, 8, 8, 8, 13, 13, 8, 13, 13, 3, 3, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 1, 1, 8, 13, 13, 8, 13, 13, 8, 3, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 8, 8] 19 rigid atoms, others: [48, 36, 37, 15, 16, 17, 18, 19, 20, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50]) total number of confs: 75 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517212 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517212 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517212/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517212 Building REAL300004517213 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517213' /scratch/stefan/7774842/working/building/REAL300004517213 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517213 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517213/0 /scratch/stefan/7774842/working/building/REAL300004517213 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 244) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/244 `/scratch/stefan/7774842/working/3D/244' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CSCCC(=O)NC1=CC=C(N2CCCCC2)C=N1) `REAL300004517213.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517213.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517213/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517213 none O=C([O-])CSCCC(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 14, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 187, 95, 71, 18, 18, 18, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 201, 201, 95, 95, 71, 71, 18, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 41]) total number of confs: 608 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517213 none O=C([O-])CSCCC(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 14, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [190, 189, 190, 118, 33, 19, 3, 3, 3, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 189, 189, 33, 33, 19, 19, 3, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 20, 21, 41, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 657 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517213 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517213 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517213/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517213 Building REAL300004517214 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517214' /scratch/stefan/7774842/working/building/REAL300004517214 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517214 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517214/0 /scratch/stefan/7774842/working/building/REAL300004517214 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 245) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/245 `/scratch/stefan/7774842/working/3D/245' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)N=C1) `REAL300004517214.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517214.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517214/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517214 none O=C([O-])C1=CC=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)N=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 8, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 1, 1, 8, 8, 8, 8, 3, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 8] 10 rigid atoms, others: [39, 9, 10, 11, 12, 13, 14, 20, 21, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40]) total number of confs: 21 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517214 none O=C([O-])C1=CC=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)N=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 8, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 8, 8, 8, 8, 10, 10, 10, 10, 10, 8, 8, 1, 1, 1, 1, 7, 8, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 8, 1] 10 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 40, 22, 23, 24, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517214 none O=C([O-])C1=CC=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)N=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 8, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 9, 9, 9, 6, 6, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 10, 10, 10, 10, 9, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 10] 10 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 39, 40]) total number of confs: 25 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517214 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517214 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517214/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517214 Building REAL300004517215 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517215' /scratch/stefan/7774842/working/building/REAL300004517215 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517215 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517215/0 /scratch/stefan/7774842/working/building/REAL300004517215 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 246) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/246 `/scratch/stefan/7774842/working/3D/246' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C(C(=O)[O-])C=C1C(=O)NC1=CC=C(N2CCCCC2)C=N1) `REAL300004517215.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517215.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517215/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517215 none CN1N=C(C(=O)[O-])C=C1C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 13, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 1, 1, 13, 13, 13, 13, 3, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1] 16 rigid atoms, others: [41, 11, 12, 13, 14, 15, 16, 22, 23, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 25 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517215 none CN1N=C(C(=O)[O-])C=C1C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 13, 13, 13, 13, 16, 16, 16, 16, 16, 13, 13, 2, 2, 2, 1, 10, 13, 13, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 13] 16 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 27] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 39 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517215 none CN1N=C(C(=O)[O-])C=C1C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 11, 11, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 16, 9, 9, 9, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 16, 16, 16, 16, 9, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6] 16 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 41]) total number of confs: 30 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517215 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517215 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517215/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517215 Building REAL300004517216 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517216' /scratch/stefan/7774842/working/building/REAL300004517216 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517216 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517216/0 /scratch/stefan/7774842/working/building/REAL300004517216 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 247) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/247 `/scratch/stefan/7774842/working/3D/247' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H](C(=O)NC2=CC=C(N3CCCCC3)C=N2)O[C@H]1C(=O)[O-]) `REAL300004517216.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517216.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517216/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517216 none C[C@@H]1C[C@H](C(=O)NC2=CC=C(N3CCCCC3)C=N2)O[C@H]1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'O.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 12, 5, 7, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 3, 17, 3, 3, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 17, 17, 17, 17, 25, 25, 17, 17, 17, 17, 17, 3, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1] 34 rigid atoms, others: [33, 34, 8, 9, 10, 11, 12, 13, 45, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 81 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517216 none C[C@@H]1C[C@H](C(=O)NC2=CC=C(N3CCCCC3)C=N2)O[C@H]1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'O.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 12, 5, 7, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 17, 17, 17, 17, 34, 34, 34, 34, 34, 17, 17, 1, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 11, 17, 17, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 17] 34 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 24, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517216 none C[C@@H]1C[C@H](C(=O)NC2=CC=C(N3CCCCC3)C=N2)O[C@H]1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'O.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 12, 5, 7, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 16, 34, 16, 16, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 16, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10] 34 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 13, 14, 15, 16, 17, 18, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 45]) total number of confs: 89 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517216 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517216 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517216/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517216 Building REAL300004517217 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517217' /scratch/stefan/7774842/working/building/REAL300004517217 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517217 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517217/0 /scratch/stefan/7774842/working/building/REAL300004517217 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 248) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/248 `/scratch/stefan/7774842/working/3D/248' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CCC(=O)[O-])C(=O)NC1=CC=C(N2CCCCC2)C=N1) `REAL300004517217.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517217 none CC(C)(CCC(=O)[O-])C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [44, 21, 44, 44, 58, 66, 66, 66, 21, 21, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 44, 44, 44, 44, 44, 44, 66, 66, 66, 66, 21, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10] 66 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 46]) total number of confs: 315 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517217 none CC(C)(CCC(=O)[O-])C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [11, 3, 11, 11, 32, 36, 53, 53, 3, 3, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 11, 11, 11, 11, 11, 11, 36, 36, 36, 36, 3, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1] 66 rigid atoms, others: [34, 35, 10, 11, 12, 13, 14, 15, 21, 22, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 238 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517217 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517217 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517217/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517217 Building REAL300004517218 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517218' /scratch/stefan/7774842/working/building/REAL300004517218 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517218 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517218/0 /scratch/stefan/7774842/working/building/REAL300004517218 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 249) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/249 `/scratch/stefan/7774842/working/3D/249' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C1) `REAL300004517218.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517218.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517218/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517218 none O=C([O-])CC1=CC=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [24, 13, 24, 13, 13, 13, 13, 3, 3, 3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 1, 1, 13, 13, 13, 13, 13, 13, 3, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 13, 13] 28 rigid atoms, others: [10, 11, 12, 13, 14, 15, 21, 22, 42, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44]) total number of confs: 64 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517218 none O=C([O-])CC1=CC=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 7, 7, 7, 13, 13, 13, 13, 28, 28, 28, 28, 28, 13, 13, 1, 1, 2, 2, 1, 1, 7, 13, 13, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 13, 1, 1] 28 rigid atoms, others: [3, 4, 5, 6, 7, 8, 43, 44, 23, 24, 27, 28] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517218 none O=C([O-])CC1=CC=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 14, 14, 14, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 9, 9, 28, 28, 28, 28, 28, 28, 14, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 28, 28] 28 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 42, 43, 44]) total number of confs: 52 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517218 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517218 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517218/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517218 Building REAL300004517219 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517219' /scratch/stefan/7774842/working/building/REAL300004517219 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517219 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517219/0 /scratch/stefan/7774842/working/building/REAL300004517219 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 250) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/250 `/scratch/stefan/7774842/working/3D/250' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=CC1=CC=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C1) `REAL300004517219.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517219.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517219/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517219 none O=C([O-])C=CC1=CC=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [39, 22, 39, 22, 13, 13, 13, 13, 3, 3, 3, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 13, 13, 22, 22, 13, 13, 3, 1, 1, 10, 10, 10, 11, 10, 10, 10, 11, 10, 10, 1, 13, 13] 48 rigid atoms, others: [32, 43, 11, 12, 13, 14, 15, 16, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45]) total number of confs: 127 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517219 none O=C([O-])C=CC1=CC=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [11, 3, 11, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 13, 13, 13, 13, 48, 48, 48, 48, 48, 13, 13, 1, 1, 3, 3, 1, 1, 7, 13, 13, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 13, 1, 1] 48 rigid atoms, others: [4, 5, 6, 7, 8, 9, 44, 45, 24, 25, 28, 29] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 99 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517219 none O=C([O-])C=CC1=CC=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 48, 48, 48, 19, 19, 19, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 48, 48, 48, 48, 48, 48, 19, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 48, 48] 48 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 43, 44, 45]) total number of confs: 86 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517219 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517219 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517219/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517219 Building REAL300004517220 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517220' /scratch/stefan/7774842/working/building/REAL300004517220 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517220 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517220/0 /scratch/stefan/7774842/working/building/REAL300004517220 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 251) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/251 `/scratch/stefan/7774842/working/3D/251' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=COC(C=CC(=O)NC2=CC=C(N3CCCCC3)C=N2)=C1) `REAL300004517220.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517220.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517220/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517220 none O=C([O-])C1=COC(C=CC(=O)NC2=CC=C(N3CCCCC3)C=N2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 12, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [65, 65, 65, 65, 65, 65, 18, 18, 3, 3, 3, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 65, 65, 18, 18, 3, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 65] 72 rigid atoms, others: [41, 11, 12, 13, 14, 15, 16, 22, 23, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42]) total number of confs: 113 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517220 none O=C([O-])C1=COC(C=CC(=O)NC2=CC=C(N3CCCCC3)C=N2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 12, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 47, 48, 48, 65, 65, 65, 65, 72, 72, 72, 72, 72, 65, 65, 1, 1, 13, 13, 48, 65, 65, 72, 72, 72, 72, 72, 72, 72, 72, 72, 72, 65, 1] 72 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 42, 24, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517220 none O=C([O-])C1=COC(C=CC(=O)NC2=CC=C(N3CCCCC3)C=N2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 12, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 72, 72, 72, 47, 47, 17, 17, 17, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 72, 72, 47, 47, 17, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 72] 72 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 41, 42]) total number of confs: 166 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517220 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517220 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517220/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517220 Building REAL300004517221 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517221' /scratch/stefan/7774842/working/building/REAL300004517221 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517221 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517221/0 /scratch/stefan/7774842/working/building/REAL300004517221 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 252) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/252 `/scratch/stefan/7774842/working/3D/252' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CCC1=CC=CC=C1C(=O)NC1=CC=C(N2CCCCC2)C=N1) `REAL300004517221.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517221.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517221/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517221 none O=C([O-])CCC1=CC=CC=C1C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [101, 83, 94, 52, 15, 15, 15, 15, 15, 15, 3, 3, 3, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 83, 83, 52, 52, 15, 15, 15, 15, 3, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1] 135 rigid atoms, others: [35, 36, 13, 14, 15, 16, 17, 18, 24, 25, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 433 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517221 none O=C([O-])CCC1=CC=CC=C1C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [23, 12, 20, 6, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 15, 15, 15, 15, 70, 70, 70, 70, 70, 15, 15, 12, 12, 6, 6, 1, 1, 1, 1, 9, 15, 15, 70, 70, 70, 70, 70, 70, 70, 70, 70, 70, 15] 135 rigid atoms, others: [32, 33, 4, 5, 6, 7, 8, 9, 10, 11, 30, 31] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517221 none O=C([O-])CCC1=CC=CC=C1C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [135, 135, 135, 118, 70, 70, 70, 70, 70, 70, 21, 21, 21, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 135, 135, 118, 118, 70, 70, 70, 70, 21, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10] 135 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 47]) total number of confs: 460 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517221 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517221 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517221/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517221 Building REAL300004517222 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517222' /scratch/stefan/7774842/working/building/REAL300004517222 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517222 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517222/0 /scratch/stefan/7774842/working/building/REAL300004517222 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 253) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/253 `/scratch/stefan/7774842/working/3D/253' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(COCC(=O)NC2=CC=C(N3CCCCC3)C=N2)OC=N1) `REAL300004517222.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517222.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517222/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517222 none O=C([O-])C1=C(COCC(=O)NC2=CC=C(N3CCCCC3)C=N2)OC=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 5, 12, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [194, 189, 194, 189, 137, 53, 16, 3, 3, 3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 1, 1, 189, 189, 189, 137, 137, 16, 16, 3, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 189] 201 rigid atoms, others: [32, 43, 10, 11, 12, 13, 14, 15, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44]) total number of confs: 594 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517222 none O=C([O-])C1=C(COCC(=O)NC2=CC=C(N3CCCCC3)C=N2)OC=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 5, 12, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 5, 26, 73, 151, 151, 151, 189, 189, 189, 189, 201, 201, 201, 201, 201, 189, 189, 1, 1, 1, 5, 5, 73, 73, 151, 189, 189, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 189, 1] 201 rigid atoms, others: [1, 3, 4, 5, 44, 23, 24, 25] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 569 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517222 none O=C([O-])C1=C(COCC(=O)NC2=CC=C(N3CCCCC3)C=N2)OC=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 5, 12, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 12, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 161, 93, 39, 13, 13, 13, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 9, 9, 201, 201, 201, 161, 161, 39, 39, 13, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 201] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 43, 44]) total number of confs: 610 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517222 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517222 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517222/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517222 Building REAL300004517223 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517223' /scratch/stefan/7774842/working/building/REAL300004517223 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517223 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517223/0 /scratch/stefan/7774842/working/building/REAL300004517223 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 254) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/254 `/scratch/stefan/7774842/working/3D/254' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=CC(=O)NC2=CC=C(N3CCCCC3)C=N2)O1) `REAL300004517223.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517223.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517223/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517223 none O=C([O-])C1=CC=C(C=CC(=O)NC2=CC=C(N3CCCCC3)C=N2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 53, 53, 53, 18, 18, 3, 3, 3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 1, 1, 53, 53, 53, 18, 18, 3, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1] 56 rigid atoms, others: [42, 11, 12, 13, 14, 15, 16, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 100 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517223 none O=C([O-])C1=CC=C(C=CC(=O)NC2=CC=C(N3CCCCC3)C=N2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 11, 11, 39, 39, 40, 53, 53, 53, 53, 56, 56, 56, 56, 56, 53, 53, 1, 1, 1, 11, 11, 40, 53, 53, 56, 56, 56, 56, 56, 56, 56, 56, 56, 56, 53] 56 rigid atoms, others: [1, 3, 4, 5, 6, 7, 24, 25, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517223 none O=C([O-])C1=CC=C(C=CC(=O)NC2=CC=C(N3CCCCC3)C=N2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 12, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 56, 56, 56, 56, 35, 35, 13, 13, 13, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 9, 9, 56, 56, 56, 35, 35, 13, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9] 56 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 42]) total number of confs: 121 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517223 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517223 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517223/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517223 Building REAL300004517224 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517224' /scratch/stefan/7774842/working/building/REAL300004517224 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517224 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517224/0 /scratch/stefan/7774842/working/building/REAL300004517224 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 255) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/255 `/scratch/stefan/7774842/working/3D/255' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])[C@@H]1CC[C@H](C(=O)NC2=CC=C(N3CCCCC3)C=N2)C1) `REAL300004517224.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517224/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517224 none O=C([O-])[C@@H]1CC[C@H](C(=O)NC2=CC=C(N3CCCCC3)C=N2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [34, 20, 34, 20, 20, 20, 20, 3, 20, 3, 3, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 1, 1, 20, 20, 20, 20, 20, 3, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 20, 20] 47 rigid atoms, others: [42, 11, 12, 13, 14, 15, 16, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44]) total number of confs: 112 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517224 none O=C([O-])[C@@H]1CC[C@H](C(=O)NC2=CC=C(N3CCCCC3)C=N2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 20, 20, 20, 20, 47, 47, 47, 47, 47, 20, 20, 1, 1, 1, 1, 1, 11, 20, 20, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 20, 1, 1] 47 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 43, 44, 24, 25, 26, 27, 28] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 88 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517224 none O=C([O-])[C@@H]1CC[C@H](C(=O)NC2=CC=C(N3CCCCC3)C=N2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 47, 47, 47, 14, 47, 14, 14, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 47, 47, 47, 47, 47, 14, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 47, 47] 47 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 42, 43, 44]) total number of confs: 108 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517224 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517224 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517224/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517224 Building REAL300004517225 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517225' /scratch/stefan/7774842/working/building/REAL300004517225 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517225 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517225/0 /scratch/stefan/7774842/working/building/REAL300004517225 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 256) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/256 `/scratch/stefan/7774842/working/3D/256' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C1C(=O)[O-]) `REAL300004517225.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517225.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517225/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517225 none CC1=CC=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [12, 12, 12, 12, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 1, 1, 12, 12, 12, 22, 22, 12, 12, 12, 12, 12, 3, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 12] 37 rigid atoms, others: [32, 43, 7, 8, 9, 10, 11, 12, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44]) total number of confs: 64 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517225 none CC1=CC=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 7, 7, 12, 12, 12, 12, 37, 37, 37, 37, 37, 12, 12, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 7, 12, 12, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 12, 1] 37 rigid atoms, others: [0, 1, 2, 3, 4, 5, 44, 20, 21, 22, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517225 none CC1=CC=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 12, 12, 12, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 12, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 37] 37 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 43, 44]) total number of confs: 66 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517225 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517225 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517225/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517225 Building REAL300004517226 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517226' /scratch/stefan/7774842/working/building/REAL300004517226 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517226 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517226/0 /scratch/stefan/7774842/working/building/REAL300004517226 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 257) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/257 `/scratch/stefan/7774842/working/3D/257' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN=CC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=C1) `REAL300004517226.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517226/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517226 none O=C([O-])C1=CN=CC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 1, 1, 9, 9, 9, 3, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 9] 21 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 21, 22, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40]) total number of confs: 23 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517226 none O=C([O-])C1=CN=CC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 9, 9, 21, 21, 21, 21, 21, 9, 9, 1, 1, 1, 5, 9, 9, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 9, 1] 21 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 40, 23, 24, 25] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517226 none O=C([O-])C1=CN=CC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 11, 11, 11, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 21, 21, 21, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 21] 21 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 39, 40]) total number of confs: 38 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517226 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517226 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517226/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517226 Building REAL300004517227 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517227' /scratch/stefan/7774842/working/building/REAL300004517227 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517227 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517227/0 /scratch/stefan/7774842/working/building/REAL300004517227 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 258) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/258 `/scratch/stefan/7774842/working/3D/258' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=C(C(=O)[O-])C=C1C(=O)NC1=CC=C(N2CCCCC2)C=N1) `REAL300004517227.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517227/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517227 none CC1=NC=C(C(=O)[O-])C=C1C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 1, 1, 17, 17, 17, 17, 17, 3, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1] 26 rigid atoms, others: [32, 43, 12, 13, 14, 15, 16, 17, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 32 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517227 none CC1=NC=C(C(=O)[O-])C=C1C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 17, 17, 17, 17, 26, 26, 26, 26, 26, 17, 17, 2, 2, 2, 1, 1, 10, 17, 17, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 17] 26 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517227 none CC1=NC=C(C(=O)[O-])C=C1C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 26, 26, 14, 14, 14, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 9, 9, 26, 26, 26, 26, 26, 14, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9] 26 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 43]) total number of confs: 51 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517227 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517227 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517227/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517227 Building REAL300004517228 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517228' /scratch/stefan/7774842/working/building/REAL300004517228 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517228 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517228/0 /scratch/stefan/7774842/working/building/REAL300004517228 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 259) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/259 `/scratch/stefan/7774842/working/3D/259' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=NN(CC(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C1) `REAL300004517228.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517228.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517228/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517228 none O=C([O-])C1=NN(CC(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 82, 82, 82, 23, 3, 3, 3, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 1, 1, 82, 82, 23, 23, 3, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 82, 82] 122 rigid atoms, others: [39, 9, 10, 11, 12, 13, 14, 20, 21, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41]) total number of confs: 160 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517228 none O=C([O-])C1=NN(CC(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 9, 54, 54, 54, 82, 82, 82, 82, 122, 122, 122, 122, 122, 82, 82, 1, 1, 9, 9, 54, 82, 82, 122, 122, 122, 122, 122, 122, 122, 122, 122, 122, 82, 1, 1] 122 rigid atoms, others: [1, 3, 4, 5, 6, 40, 41, 22, 23] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 267 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517228 none O=C([O-])C1=NN(CC(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [122, 122, 122, 122, 122, 73, 21, 21, 21, 10, 10, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 122, 122, 73, 73, 21, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 122, 122] 122 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 39, 40, 41]) total number of confs: 347 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517228 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517228 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517228/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517228 Building REAL300004517229 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517229' /scratch/stefan/7774842/working/building/REAL300004517229 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517229 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517229/0 /scratch/stefan/7774842/working/building/REAL300004517229 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 260) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/260 `/scratch/stefan/7774842/working/3D/260' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=NN(CCCC(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C1) `REAL300004517229.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517229.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517229/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517229 none O=C([O-])C1=NN(CCCC(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [187, 187, 187, 187, 187, 72, 29, 19, 3, 3, 3, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 187, 187, 67, 68, 37, 37, 19, 19, 3, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 187, 187] 201 rigid atoms, others: [33, 34, 11, 12, 13, 14, 15, 16, 22, 23, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47]) total number of confs: 531 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517229 none O=C([O-])C1=NN(CCCC(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 8, 16, 34, 133, 133, 133, 187, 187, 187, 187, 201, 201, 201, 201, 201, 187, 187, 1, 1, 8, 8, 16, 16, 34, 34, 133, 187, 187, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 187, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 46, 47, 24, 25] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 560 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517229 none O=C([O-])C1=NN(CCCC(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 117, 63, 53, 14, 14, 14, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 201, 201, 111, 111, 77, 77, 53, 53, 14, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 201, 201] 201 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 45, 46, 47]) total number of confs: 715 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517229 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517229 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517229/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517229 Building REAL300004517230 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517230' /scratch/stefan/7774842/working/building/REAL300004517230 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517230 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517230/0 /scratch/stefan/7774842/working/building/REAL300004517230 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 261) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/261 `/scratch/stefan/7774842/working/3D/261' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])[C@@H]1CC[C@@H]1C(=O)NC1=CC=C(N2CCCCC2)C=N1) `REAL300004517230.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517230 none O=C([O-])[C@@H]1CC[C@@H]1C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 9, 7, 7, 7, 7, 3, 7, 3, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 1, 1, 7, 7, 7, 7, 3, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1] 13 rigid atoms, others: [41, 11, 12, 13, 14, 15, 16, 22, 23, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 35 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517230 none O=C([O-])[C@@H]1CC[C@@H]1C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 13, 13, 13, 13, 13, 7, 7, 1, 1, 1, 1, 5, 7, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7] 13 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 24, 25, 26, 27] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 30 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517230 none O=C([O-])[C@@H]1CC[C@@H]1C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 10, 13, 10, 10, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 13, 13, 13, 13, 10, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8] 13 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 41]) total number of confs: 27 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517230 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517230 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517230/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517230 Building REAL300004517231 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517231' /scratch/stefan/7774842/working/building/REAL300004517231 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517231 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517231/0 /scratch/stefan/7774842/working/building/REAL300004517231 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 262) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/262 `/scratch/stefan/7774842/working/3D/262' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC[C@@H]1CC[C@H](C(=O)NC2=CC=C(N3CCCCC3)C=N2)O1) `REAL300004517231.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517231 none O=C([O-])CC[C@@H]1CC[C@H](C(=O)NC2=CC=C(N3CCCCC3)C=N2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 7, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [105, 96, 105, 70, 19, 19, 19, 19, 19, 3, 19, 3, 3, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 19, 96, 96, 70, 70, 19, 19, 19, 19, 3, 1, 1, 10, 10, 10, 11, 10, 11, 10, 11, 11, 10, 1] 120 rigid atoms, others: [48, 36, 37, 13, 14, 15, 16, 17, 18, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 442 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517231 none O=C([O-])CC[C@@H]1CC[C@H](C(=O)NC2=CC=C(N3CCCCC3)C=N2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 7, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [27, 17, 27, 8, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 19, 19, 19, 19, 58, 58, 58, 58, 58, 19, 19, 1, 17, 17, 8, 8, 1, 1, 1, 1, 10, 19, 19, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 19] 120 rigid atoms, others: [32, 33, 34, 4, 5, 6, 7, 8, 9, 10, 11, 26, 31] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517231 none O=C([O-])CC[C@@H]1CC[C@H](C(=O)NC2=CC=C(N3CCCCC3)C=N2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 7, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [120, 120, 120, 106, 58, 58, 58, 58, 58, 19, 58, 19, 19, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 58, 120, 120, 106, 106, 58, 58, 58, 58, 19, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10] 120 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48]) total number of confs: 452 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517231 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517231 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517231/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517231 Building REAL300004517232 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517232' /scratch/stefan/7774842/working/building/REAL300004517232 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517232 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517232/0 /scratch/stefan/7774842/working/building/REAL300004517232 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 263) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/263 `/scratch/stefan/7774842/working/3D/263' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])[C@@H]1CO[C@H](CCC(=O)NC2=CC=C(N3CCCCC3)C=N2)C1) `REAL300004517232.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517232 none O=C([O-])[C@@H]1CO[C@H](CCC(=O)NC2=CC=C(N3CCCCC3)C=N2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 12, 5, 7, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [171, 122, 171, 122, 122, 122, 122, 34, 122, 19, 3, 3, 3, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 122, 122, 122, 42, 42, 19, 19, 3, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 122, 122] 195 rigid atoms, others: [34, 35, 13, 14, 15, 16, 17, 18, 46, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 616 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517232 none O=C([O-])[C@@H]1CO[C@H](CCC(=O)NC2=CC=C(N3CCCCC3)C=N2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 12, 5, 7, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 8, 16, 79, 79, 79, 122, 122, 122, 122, 195, 195, 195, 195, 195, 122, 122, 1, 1, 1, 8, 8, 16, 16, 79, 122, 122, 195, 195, 195, 195, 195, 195, 195, 195, 195, 195, 122, 1, 1] 195 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 47, 48, 26, 27, 28] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 440 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517232 none O=C([O-])[C@@H]1CO[C@H](CCC(=O)NC2=CC=C(N3CCCCC3)C=N2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 12, 5, 7, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [195, 195, 195, 195, 195, 195, 195, 119, 195, 94, 21, 21, 21, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 195, 195, 195, 137, 137, 94, 94, 21, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 195, 195] 195 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 46, 47, 48]) total number of confs: 798 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517232 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517232 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517232/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517232 Building REAL300004517233 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517233' /scratch/stefan/7774842/working/building/REAL300004517233 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517233 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517233/0 /scratch/stefan/7774842/working/building/REAL300004517233 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 264) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/264 `/scratch/stefan/7774842/working/3D/264' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])[C@@H]1CC[C@@H]1C(=O)NC1=CC=C(N2CCCCC2)C=N1) `REAL300004517233.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517233.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517233/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517233 none O=C([O-])[C@@H]1CC[C@@H]1C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 9, 7, 7, 7, 7, 3, 7, 3, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 1, 1, 7, 7, 7, 7, 3, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1] 13 rigid atoms, others: [41, 11, 12, 13, 14, 15, 16, 22, 23, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 35 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517233 none O=C([O-])[C@@H]1CC[C@@H]1C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 7, 7, 7, 7, 13, 13, 13, 13, 13, 7, 7, 1, 1, 1, 1, 5, 7, 7, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7] 13 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 24, 25, 26, 27] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 30 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517233 none O=C([O-])[C@@H]1CC[C@@H]1C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 10, 13, 10, 10, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 13, 13, 13, 13, 10, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8] 13 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 41]) total number of confs: 27 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517233 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517233 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517233/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517233 Building REAL300004517234 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517234' /scratch/stefan/7774842/working/building/REAL300004517234 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517234 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517234/0 /scratch/stefan/7774842/working/building/REAL300004517234 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 265) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/265 `/scratch/stefan/7774842/working/3D/265' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)OC(C(=O)[O-])=C1) `REAL300004517234.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517234.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517234/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517234 none CC1=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)OC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 12, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 3, 3, 3, 1, 1, 1, 1, 1, 1, 9, 9, 8, 9, 9, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 3, 1, 1, 9, 9, 9, 9, 8, 9, 9, 9, 9, 9, 1, 15] 20 rigid atoms, others: [5, 6, 7, 8, 9, 10, 16, 17, 40, 28, 29] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41]) total number of confs: 35 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517234 none CC1=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)OC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 12, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 9, 9, 10, 15, 15, 15, 15, 20, 20, 20, 20, 20, 15, 15, 1, 1, 1, 2, 2, 1, 2, 2, 2, 10, 15, 15, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 15, 1] 20 rigid atoms, others: [0, 1, 2, 3, 41, 18, 19, 20, 23] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517234 none CC1=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)OC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 12, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 12, 12, 12, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 20, 20, 20, 20, 20, 20, 20, 20, 20, 12, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 20] 20 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 40, 41]) total number of confs: 44 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517234 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517234 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517234/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517234 Building REAL300004517235 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517235' /scratch/stefan/7774842/working/building/REAL300004517235 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517235 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517235/0 /scratch/stefan/7774842/working/building/REAL300004517235 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 266) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/266 `/scratch/stefan/7774842/working/3D/266' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])[C@H]1C2C=CC(CC2)[C@H]1C(=O)NC1=CC=C(N2CCCCC2)C=N1) `REAL300004517235.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517235.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517235/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517235 none O=C([O-])[C@H]1C2C=CC(CC2)[C@H]1C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 1, 1, 5, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 5, 3, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 3, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1] 8 rigid atoms, others: [37, 38, 49, 15, 16, 17, 18, 19, 20, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 20 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517235 none O=C([O-])[C@H]1C2C=CC(CC2)[C@H]1C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 1, 1, 5, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 5, 5, 5, 5, 8, 8, 8, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 4, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5] 8 rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 35, 33, 28, 29, 30, 31] set([0, 2, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517235 none O=C([O-])[C@H]1C2C=CC(CC2)[C@H]1C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 1, 1, 5, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 8, 8, 8, 8, 7, 8, 7, 7, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 8, 8, 8, 8, 8, 8, 7, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5] 8 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 49]) total number of confs: 18 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517235 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517235 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517235/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517235 Building REAL300004517236 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517236' /scratch/stefan/7774842/working/building/REAL300004517236 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517236 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517236/0 /scratch/stefan/7774842/working/building/REAL300004517236 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 267) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/267 `/scratch/stefan/7774842/working/3D/267' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(C(=O)[O-])C(=O)NC1=CC=C(N2CCCCC2)C=N1) `REAL300004517236.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517236.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517236/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517236 none CC(C)C(C(=O)[O-])C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [30, 26, 30, 13, 26, 26, 26, 13, 13, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 30, 30, 30, 30, 30, 30, 30, 26, 13, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8] 30 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 43]) total number of confs: 107 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517236 none CC(C)C(C(=O)[O-])C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [20, 12, 19, 3, 12, 17, 17, 3, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 1, 1, 20, 20, 20, 20, 20, 20, 20, 12, 3, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1] 30 rigid atoms, others: [32, 43, 9, 10, 11, 12, 13, 14, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517236 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517236 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517236/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517236 Building REAL300004517237 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517237' /scratch/stefan/7774842/working/building/REAL300004517237 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517237 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517237/0 /scratch/stefan/7774842/working/building/REAL300004517237 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 268) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/268 `/scratch/stefan/7774842/working/3D/268' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])[C@@H]1CCCC[C@@H]1C(=O)NC1=CC=C(N2CCCCC2)C=N1) `REAL300004517237.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517237.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517237/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517237 none O=C([O-])[C@@H]1CCCC[C@@H]1C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 6, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 3, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1] 10 rigid atoms, others: [35, 36, 13, 14, 15, 16, 17, 18, 24, 25, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 21 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517237 none O=C([O-])[C@@H]1CCCC[C@@H]1C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 6, 6, 6, 6, 10, 10, 10, 10, 10, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 5, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6] 10 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 33, 26, 27, 28, 29, 30, 31] set([0, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 25 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517237 none O=C([O-])[C@@H]1CCCC[C@@H]1C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 5, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 10, 10, 8, 10, 8, 8, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 8, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6] 10 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 47]) total number of confs: 21 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517237 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517237 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517237/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517237 Building REAL300004517238 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517238' /scratch/stefan/7774842/working/building/REAL300004517238 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300004517238 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517238/0 /scratch/stefan/7774842/working/building/REAL300004517238 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 269) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/269 `/scratch/stefan/7774842/working/3D/269' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1CCCN(CC(=O)NC2=CC=C(N3CCCCC3)C=N2)C1) `REAL300004517238.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517238 none O=C([O-])C1CCCN(CC(=O)NC2=CC=C(N3CCCCC3)C=N2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 10, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [74, 48, 74, 48, 48, 48, 48, 22, 3, 3, 3, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 48, 48, 48, 48, 48, 48, 48, 48, 22, 22, 3, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 48, 48] 90 rigid atoms, others: [35, 36, 11, 12, 13, 14, 15, 16, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49]) total number of confs: 223 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517238 none O=C([O-])C1CCCN(CC(=O)NC2=CC=C(N3CCCCC3)C=N2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 10, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 10, 31, 31, 31, 48, 48, 48, 48, 90, 90, 90, 90, 90, 48, 48, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 31, 48, 48, 90, 90, 90, 90, 90, 90, 90, 90, 90, 90, 48, 1, 1] 90 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 48, 49, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517238 none O=C([O-])C1CCCN(CC(=O)NC2=CC=C(N3CCCCC3)C=N2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 10, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [90, 90, 90, 90, 90, 90, 90, 71, 20, 20, 20, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 90, 90, 90, 90, 90, 90, 90, 90, 71, 71, 20, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 90, 90] 90 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 47, 48, 49]) total number of confs: 282 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517238 /scratch/stefan/7774842/working /scratch/stefan/7774842 mkdir: created directory `1' /scratch/stefan/7774842/working/building/REAL300004517238/1 /scratch/stefan/7774842/working/building/REAL300004517238 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 1 (index: 270) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/270 `/scratch/stefan/7774842/working/3D/270' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1CCC[N@H+](CC(=O)NC2=CC=C(N3CCCCC3)C=N2)C1) `REAL300004517238.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004517238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517238/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517238 none O=C([O-])C1CCC[N@H+](CC(=O)NC2=CC=C(N3CCCCC3)C=N2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [82, 54, 82, 54, 54, 54, 52, 19, 54, 3, 3, 3, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 54, 54, 54, 54, 54, 54, 54, 54, 19, 19, 3, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 54, 54] 106 rigid atoms, others: [48, 36, 37, 12, 13, 14, 15, 16, 17, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50]) total number of confs: 299 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517238 none O=C([O-])C1CCC[N@H+](CC(=O)NC2=CC=C(N3CCCCC3)C=N2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 10, 31, 31, 31, 54, 54, 54, 54, 106, 106, 106, 106, 106, 54, 54, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 31, 54, 54, 106, 106, 106, 106, 106, 106, 106, 106, 106, 106, 54, 1, 1] 106 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 49, 50, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517238 none O=C([O-])C1CCC[N@H+](CC(=O)NC2=CC=C(N3CCCCC3)C=N2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [106, 106, 106, 106, 106, 106, 103, 68, 106, 19, 19, 19, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 106, 106, 106, 106, 106, 106, 106, 106, 68, 68, 19, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 106, 106] 106 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49, 50]) total number of confs: 390 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517238 /scratch/stefan/7774842/working /scratch/stefan/7774842 mkdir: created directory `2' /scratch/stefan/7774842/working/building/REAL300004517238/2 /scratch/stefan/7774842/working/building/REAL300004517238 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 2 (index: 271) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/271 `/scratch/stefan/7774842/working/3D/271' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1CCC[N@@H+](CC(=O)NC2=CC=C(N3CCCCC3)C=N2)C1) `REAL300004517238.mol2' -> `2.mol2' `temp.mol2' -> `REAL300004517238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517238/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517238 none O=C([O-])C1CCC[N@@H+](CC(=O)NC2=CC=C(N3CCCCC3)C=N2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [83, 55, 83, 55, 55, 55, 54, 19, 55, 3, 3, 3, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 1, 1, 55, 55, 55, 55, 55, 55, 55, 55, 19, 19, 3, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 55, 55] 107 rigid atoms, others: [48, 36, 37, 12, 13, 14, 15, 16, 17, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50]) total number of confs: 297 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517238 none O=C([O-])C1CCC[N@@H+](CC(=O)NC2=CC=C(N3CCCCC3)C=N2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 10, 32, 32, 32, 55, 55, 55, 55, 107, 107, 107, 107, 107, 55, 55, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 32, 55, 55, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107, 55, 1, 1] 107 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 49, 50, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 224 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517238 none O=C([O-])C1CCC[N@@H+](CC(=O)NC2=CC=C(N3CCCCC3)C=N2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 1, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 107 conformations in input total number of sets (complete confs): 107 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 107, 107, 107, 106, 66, 107, 19, 19, 19, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 107, 107, 107, 107, 107, 107, 107, 107, 66, 66, 19, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 107, 107] 107 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49, 50]) total number of confs: 377 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517238 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517238 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 2: /scratch/stefan/7774842/working/building/REAL300004517238/2.* 1: /scratch/stefan/7774842/working/building/REAL300004517238/1.* 0: /scratch/stefan/7774842/working/building/REAL300004517238/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517238 Building REAL300004517239 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517239' /scratch/stefan/7774842/working/building/REAL300004517239 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517239 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517239/0 /scratch/stefan/7774842/working/building/REAL300004517239 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 272) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/272 `/scratch/stefan/7774842/working/3D/272' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1(C(=O)NC2=CC=C(N3CCCCC3)C=N2)CC1C1=CC=CC=C1) `REAL300004517239.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517239.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517239/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2', 'output.4.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517239 none O=C([O-])C1(C(=O)NC2=CC=C(N3CCCCC3)C=N2)CC1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [14, 8, 14, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 3, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 8, 8, 8, 8, 8, 8, 8, 8] 23 rigid atoms, others: [6, 7, 8, 9, 10, 11, 17, 18, 40, 28, 29] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 51 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.4.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.4.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517239 none O=C([O-])C1(C(=O)NC2=CC=C(N3CCCCC3)C=N2)CC1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 2, 2, 5, 5, 5, 8, 8, 8, 8, 23, 23, 23, 23, 23, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 8, 2, 2, 2, 1, 1, 1, 1, 1] 23 rigid atoms, others: [44, 45, 46, 47, 48, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 44 number of broken/clashed sets: 1 ./output.4.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517239 none O=C([O-])C1(C(=O)NC2=CC=C(N3CCCCC3)C=N2)CC1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 5, 5, 5, 8, 8, 8, 8, 23, 23, 23, 23, 23, 8, 8, 1, 1, 1, 2, 2, 2, 2, 2, 5, 8, 8, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 8, 1, 1, 1, 2, 2, 2, 2, 2] 23 rigid atoms, others: [1, 3, 4, 41, 42, 43, 19, 20, 21] set([0, 2, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44, 45, 46, 47, 48]) total number of confs: 46 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517239 none O=C([O-])C1(C(=O)NC2=CC=C(N3CCCCC3)C=N2)CC1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 5, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 13, 13, 13, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 23, 23, 23, 23, 23, 23, 23, 23, 13, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 23, 23, 23, 23, 23, 23, 23, 23] 23 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 63 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517239 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517239 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517239/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517239 Building REAL300004517240 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517240' /scratch/stefan/7774842/working/building/REAL300004517240 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517240 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517240/0 /scratch/stefan/7774842/working/building/REAL300004517240 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 273) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/273 `/scratch/stefan/7774842/working/3D/273' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)NC2=CC=CC=C21) `REAL300004517240.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517240.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517240/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517240 none O=C([O-])CC1=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)NC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [16, 14, 16, 12, 12, 3, 3, 3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 1, 1, 12, 12, 12, 12, 12, 12, 12, 14, 14, 3, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 12, 12, 12, 12, 12] 21 rigid atoms, others: [32, 43, 8, 9, 10, 11, 12, 13, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48]) total number of confs: 47 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517240 none O=C([O-])CC1=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)NC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 1, 1, 1, 1, 8, 8, 8, 12, 12, 12, 12, 19, 19, 19, 19, 19, 12, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 12, 12, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 12, 1, 1, 1, 1, 1] 21 rigid atoms, others: [3, 4, 5, 6, 44, 45, 46, 47, 48, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517240 none O=C([O-])CC1=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)NC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 19, 19, 14, 14, 14, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 9, 9, 19, 19, 19, 19, 19, 19, 19, 21, 21, 14, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 19, 19, 19, 19, 19] 21 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 43, 44, 45, 46, 47, 48]) total number of confs: 51 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517240 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517240 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517240/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517240 Building REAL300004517241 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517241' /scratch/stefan/7774842/working/building/REAL300004517241 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517241 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517241/0 /scratch/stefan/7774842/working/building/REAL300004517241 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 274) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/274 `/scratch/stefan/7774842/working/3D/274' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN(CC(=O)NC2=CC=C(N3CCCCC3)C=N2)C2=CC=CC=C12) `REAL300004517241.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517241.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517241/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517241 none O=C([O-])C1=CN(CC(=O)NC2=CC=C(N3CCCCC3)C=N2)C2=CC=CC=C12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 114 conformations in input total number of sets (complete confs): 114 using faster count positions algorithm for large data unique positions, atoms: [101, 77, 101, 77, 77, 21, 3, 3, 3, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 77, 77, 77, 77, 77, 77, 77, 21, 21, 3, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 77, 77, 77, 77] 114 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 44, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48]) total number of confs: 248 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517241 none O=C([O-])C1=CN(CC(=O)NC2=CC=C(N3CCCCC3)C=N2)C2=CC=CC=C12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 114 conformations in input total number of sets (complete confs): 114 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 8, 47, 47, 47, 77, 77, 77, 77, 114, 114, 114, 114, 114, 77, 77, 1, 1, 1, 1, 1, 1, 1, 8, 8, 47, 77, 77, 114, 114, 114, 114, 114, 114, 114, 114, 114, 114, 77, 1, 1, 1, 1] 114 rigid atoms, others: [1, 3, 4, 5, 6, 45, 46, 47, 48, 22, 23, 24, 25, 26, 27, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 248 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517241 none O=C([O-])C1=CN(CC(=O)NC2=CC=C(N3CCCCC3)C=N2)C2=CC=CC=C12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 114 conformations in input total number of sets (complete confs): 114 using faster count positions algorithm for large data unique positions, atoms: [114, 114, 114, 114, 114, 67, 16, 16, 16, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 114, 114, 114, 114, 114, 114, 114, 67, 67, 16, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 114, 114, 114, 114] 114 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 44, 45, 46, 47, 48]) total number of confs: 298 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517241 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517241 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517241/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517241 Building REAL300004517242 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517242' /scratch/stefan/7774842/working/building/REAL300004517242 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517242 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517242/0 /scratch/stefan/7774842/working/building/REAL300004517242 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 275) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/275 `/scratch/stefan/7774842/working/3D/275' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1CC12CC(C(=O)NC1=CC=C(N3CCCCC3)C=N1)C2) `REAL300004517242.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517242.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517242/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517242 none O=C([O-])C1CC12CC(C(=O)NC1=CC=C(N3CCCCC3)C=N1)C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [36, 21, 36, 21, 21, 21, 21, 3, 3, 3, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 1, 1, 21, 21, 21, 21, 21, 21, 21, 3, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 21, 21] 47 rigid atoms, others: [32, 43, 10, 11, 12, 13, 14, 15, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45]) total number of confs: 118 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517242 none O=C([O-])C1CC12CC(C(=O)NC1=CC=C(N3CCCCC3)C=N1)C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 12, 12, 12, 21, 21, 21, 21, 47, 47, 47, 47, 47, 21, 21, 1, 1, 1, 1, 1, 1, 1, 12, 21, 21, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 21, 1, 1] 47 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 44, 45, 23, 24, 25, 26, 27, 28, 29] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 90 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517242 none O=C([O-])C1CC12CC(C(=O)NC1=CC=C(N3CCCCC3)C=N1)C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 47, 47, 47, 17, 17, 17, 10, 10, 11, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 47, 47, 47, 47, 47, 47, 47, 17, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 47, 47] 47 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 43, 44, 45]) total number of confs: 125 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517242 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517242 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517242/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517242 Building REAL300004517243 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517243' /scratch/stefan/7774842/working/building/REAL300004517243 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517243 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517243/0 /scratch/stefan/7774842/working/building/REAL300004517243 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 276) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/276 `/scratch/stefan/7774842/working/3D/276' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])[C@H]1C[C@@H](C(=O)NC2=CC=C(N3CCCCC3)C=N2)C1) `REAL300004517243.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517243/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517243 none O=C([O-])[C@H]1C[C@@H](C(=O)NC2=CC=C(N3CCCCC3)C=N2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [34, 20, 34, 20, 20, 20, 3, 20, 3, 3, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 20, 20, 20, 3, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 20, 20] 51 rigid atoms, others: [39, 10, 11, 12, 13, 14, 15, 21, 22, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41]) total number of confs: 111 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517243 none O=C([O-])[C@H]1C[C@@H](C(=O)NC2=CC=C(N3CCCCC3)C=N2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 11, 11, 11, 20, 20, 20, 20, 51, 51, 51, 51, 51, 20, 20, 1, 1, 1, 11, 20, 20, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 20, 1, 1] 51 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 41, 40, 23, 24, 25] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 92 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517243 none O=C([O-])[C@H]1C[C@@H](C(=O)NC2=CC=C(N3CCCCC3)C=N2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 51, 51, 51, 18, 51, 18, 18, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 51, 51, 51, 18, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 51, 51] 51 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 39, 40, 41]) total number of confs: 129 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517243 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517243 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517243/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517243 Building REAL300004517244 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517244' /scratch/stefan/7774842/working/building/REAL300004517244 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517244 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517244/0 /scratch/stefan/7774842/working/building/REAL300004517244 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 277) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/277 `/scratch/stefan/7774842/working/3D/277' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@]1(C(=O)[O-])C[C@@H]1C(=O)NC1=CC=C(N2CCCCC2)C=N1) `REAL300004517244.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517244 none CC(C)[C@@]1(C(=O)[O-])C[C@@H]1C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [15, 10, 15, 10, 10, 10, 10, 10, 3, 10, 3, 3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 1, 1, 15, 15, 15, 15, 15, 15, 15, 10, 10, 3, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1] 21 rigid atoms, others: [35, 36, 12, 13, 14, 15, 16, 17, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 58 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517244 none CC(C)[C@@]1(C(=O)[O-])C[C@@H]1C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 1, 1, 2, 2, 1, 1, 1, 1, 7, 7, 7, 10, 10, 10, 10, 20, 20, 20, 20, 20, 10, 10, 6, 6, 6, 6, 6, 6, 6, 1, 1, 7, 10, 10, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 10] 21 rigid atoms, others: [32, 1, 3, 4, 33, 7, 8, 9, 10] set([0, 2, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517244 none CC(C)[C@@]1(C(=O)[O-])C[C@@H]1C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 20, 21, 20, 20, 20, 20, 20, 14, 20, 14, 14, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 9, 9, 21, 21, 21, 21, 21, 21, 21, 20, 20, 14, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9] 21 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 47]) total number of confs: 58 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517244 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517244 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517244/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517244 Building REAL300004517245 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517245' /scratch/stefan/7774842/working/building/REAL300004517245 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517245 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517245/0 /scratch/stefan/7774842/working/building/REAL300004517245 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 278) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/278 `/scratch/stefan/7774842/working/3D/278' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)[O-])C=C1C(=O)NC1=CC=C(N2CCCCC2)C=N1) `REAL300004517245.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517245/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517245 none CC1=CC=C(C(=O)[O-])C=C1C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 16, 16, 3, 3, 3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 1, 1, 16, 16, 16, 16, 16, 16, 3, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1] 26 rigid atoms, others: [32, 33, 44, 12, 13, 14, 15, 16, 17, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 31 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517245 none CC1=CC=C(C(=O)[O-])C=C1C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 16, 16, 16, 16, 26, 26, 26, 26, 26, 16, 16, 2, 2, 2, 1, 1, 1, 9, 16, 16, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 16] 26 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 28, 29, 30] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517245 none CC1=CC=C(C(=O)[O-])C=C1C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 26, 26, 14, 14, 14, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 9, 9, 26, 26, 26, 26, 26, 26, 14, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9] 26 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 44]) total number of confs: 50 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517245 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517245 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517245/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517245 Building REAL300004517246 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517246' /scratch/stefan/7774842/working/building/REAL300004517246 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517246 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517246/0 /scratch/stefan/7774842/working/building/REAL300004517246 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 279) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/279 `/scratch/stefan/7774842/working/3D/279' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C(=O)[O-])CC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C1) `REAL300004517246.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517246 none CC1(C(=O)[O-])CC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 11, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 35, 35, 22, 3, 3, 3, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 22, 22, 22, 22, 22, 22, 22, 3, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 22, 22] 49 rigid atoms, others: [9, 10, 11, 12, 13, 14, 20, 21, 42, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44]) total number of confs: 111 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517246 none CC1(C(=O)[O-])CC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 11, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 1, 1, 1, 13, 13, 13, 22, 22, 22, 22, 49, 49, 49, 49, 49, 22, 22, 1, 2, 2, 2, 1, 1, 1, 13, 22, 22, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 22, 1, 1] 49 rigid atoms, others: [0, 1, 2, 5, 6, 7, 43, 44, 22, 26, 27, 28] set([3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 99 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517246 none CC1(C(=O)[O-])CC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 11, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 49, 19, 19, 19, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 49, 49, 49, 49, 49, 49, 49, 19, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 49, 49] 49 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 42, 43, 44]) total number of confs: 131 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517246 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517246 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517246/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517246 Building REAL300004517247 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517247' /scratch/stefan/7774842/working/building/REAL300004517247 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517247 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517247/0 /scratch/stefan/7774842/working/building/REAL300004517247 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 280) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/280 `/scratch/stefan/7774842/working/3D/280' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C=CS1) `REAL300004517247.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517247 none O=C([O-])C1=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [21, 15, 21, 15, 3, 3, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 1, 1, 15, 15, 15, 3, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 15, 15] 29 rigid atoms, others: [36, 7, 8, 9, 10, 11, 12, 18, 19, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 15, 16, 17, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38]) total number of confs: 53 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517247 none O=C([O-])C1=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 10, 10, 10, 15, 15, 15, 15, 29, 29, 29, 29, 29, 15, 15, 1, 1, 1, 10, 15, 15, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 15, 1, 1] 29 rigid atoms, others: [1, 3, 4, 5, 38, 20, 21, 22, 37] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517247 none O=C([O-])C1=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 13, 13, 13, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 29, 29, 29, 13, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 29, 29] 29 rigid atoms, others: [32, 33, 34, 35, 11, 12, 13, 14, 15, 16, 17, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 36, 37, 38]) total number of confs: 52 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517247 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517247 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517247/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517247 Building REAL300004517248 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517248' /scratch/stefan/7774842/working/building/REAL300004517248 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004517248 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517248/0 /scratch/stefan/7774842/working/building/REAL300004517248 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 281) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/281 `/scratch/stefan/7774842/working/3D/281' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=NNC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=C1) `REAL300004517248.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517248 none O=C([O-])C1=NNC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 12, 3, 3, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 1, 1, 12, 12, 3, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 12] 16 rigid atoms, others: [37, 9, 10, 11, 12, 13, 14, 20, 21, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38]) total number of confs: 25 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517248 none O=C([O-])C1=NNC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 8, 9, 12, 12, 12, 12, 16, 16, 16, 16, 16, 12, 12, 1, 1, 9, 12, 12, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 12, 1] 16 rigid atoms, others: [1, 3, 4, 5, 6, 7, 22, 23, 38] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517248 none O=C([O-])C1=NNC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 10, 10, 10, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 16, 16, 10, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 16] 16 rigid atoms, others: [32, 33, 34, 35, 36, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 37, 38]) total number of confs: 29 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517248 /scratch/stefan/7774842/working /scratch/stefan/7774842 mkdir: created directory `1' /scratch/stefan/7774842/working/building/REAL300004517248/1 /scratch/stefan/7774842/working/building/REAL300004517248 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 1 (index: 282) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/282 `/scratch/stefan/7774842/working/3D/282' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=NN1) `REAL300004517248.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004517248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517248/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517248 none O=C([O-])C1=CC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=NN1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 8, 8, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 1, 1, 12, 12, 12, 3, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 12] 17 rigid atoms, others: [37, 8, 9, 10, 11, 12, 13, 19, 20, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38]) total number of confs: 24 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517248 none O=C([O-])C1=CC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=NN1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 8, 8, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 8, 8, 9, 12, 12, 12, 12, 17, 17, 17, 17, 17, 12, 12, 1, 1, 1, 9, 12, 12, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 12, 1] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 21, 22, 23, 38] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517248 none O=C([O-])C1=CC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=NN1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 8, 8, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 9, 9, 9, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 17, 17, 17, 9, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 17] 17 rigid atoms, others: [32, 33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 37, 38]) total number of confs: 31 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517248 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517248 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 1: /scratch/stefan/7774842/working/building/REAL300004517248/1.* 0: /scratch/stefan/7774842/working/building/REAL300004517248/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517248 Building REAL300004517249 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517249' /scratch/stefan/7774842/working/building/REAL300004517249 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517249 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517249/0 /scratch/stefan/7774842/working/building/REAL300004517249 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 283) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/283 `/scratch/stefan/7774842/working/3D/283' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=NC=C1C(=O)NC1=CC=C(N2CCCCC2)C=N1) `REAL300004517249.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517249.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517249/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517249 none CC1=C(C(=O)[O-])C=NC=C1C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 8, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 16, 16, 3, 3, 3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 1, 1, 16, 16, 16, 16, 16, 3, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1] 22 rigid atoms, others: [32, 43, 12, 13, 14, 15, 16, 17, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 31 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517249 none CC1=C(C(=O)[O-])C=NC=C1C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 8, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 10, 10, 10, 16, 16, 16, 16, 22, 22, 22, 22, 22, 16, 16, 2, 2, 2, 1, 1, 10, 16, 16, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 16] 22 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 9, 10, 28, 29] set([4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517249 none CC1=C(C(=O)[O-])C=NC=C1C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 8, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 22, 13, 13, 13, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 9, 9, 22, 22, 22, 22, 22, 13, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9] 22 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 43]) total number of confs: 41 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517249 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517249 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517249/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517249 Building REAL300004517250 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517250' /scratch/stefan/7774842/working/building/REAL300004517250 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517250 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517250/0 /scratch/stefan/7774842/working/building/REAL300004517250 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 284) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/284 `/scratch/stefan/7774842/working/3D/284' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C(=O)[O-])C(=O)NC1=CC=C(N2CCCCC2)C=N1) `REAL300004517250.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517250.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517250/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517250 none CCCC(C(=O)[O-])C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [95, 91, 62, 20, 62, 70, 70, 20, 20, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 95, 95, 95, 93, 95, 94, 94, 62, 20, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10] 95 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 43]) total number of confs: 432 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517250 none CCCC(C(=O)[O-])C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [56, 46, 16, 3, 16, 25, 25, 3, 3, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 56, 56, 56, 54, 56, 49, 49, 16, 3, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1] 95 rigid atoms, others: [32, 43, 9, 10, 11, 12, 13, 14, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 281 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517250 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517250 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517250/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517250 Building REAL300004517251 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517251' /scratch/stefan/7774842/working/building/REAL300004517251 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517251 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517251/0 /scratch/stefan/7774842/working/building/REAL300004517251 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 285) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/285 `/scratch/stefan/7774842/working/3D/285' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1C(=O)NC1=CC=C(N2CCCCC2)C=N1) `REAL300004517251.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517251 none CC1=CC(C(=O)[O-])=CC=C1C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 4, 17, 17, 17, 17, 17, 3, 3, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 1, 1, 17, 17, 17, 17, 17, 17, 3, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1] 19 rigid atoms, others: [32, 33, 44, 12, 13, 14, 15, 16, 17, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 65 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517251 none CC1=CC(C(=O)[O-])=CC=C1C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 10, 10, 10, 17, 17, 17, 17, 19, 19, 19, 19, 19, 17, 17, 2, 2, 2, 1, 1, 1, 10, 17, 17, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 17] 19 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 28, 29, 30] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517251 none CC1=CC(C(=O)[O-])=CC=C1C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 19, 19, 11, 11, 11, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 19, 19, 19, 19, 19, 19, 11, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7] 19 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 44]) total number of confs: 35 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517251 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517251 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517251/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517251 Building REAL300004517252 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517252' /scratch/stefan/7774842/working/building/REAL300004517252 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517252 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517252/0 /scratch/stefan/7774842/working/building/REAL300004517252 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 286) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/286 `/scratch/stefan/7774842/working/3D/286' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C(Cl)=C1) `REAL300004517252.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517252 none O=C([O-])C1=CC=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 16, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 5, 12, 12, 3, 3, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 12, 12, 12, 12, 12, 3, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 12] 15 rigid atoms, others: [40, 9, 10, 11, 12, 13, 14, 20, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41]) total number of confs: 49 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517252 none O=C([O-])C1=CC=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 16, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 12, 12, 12, 12, 15, 15, 15, 15, 15, 12, 12, 1, 1, 1, 1, 1, 7, 12, 12, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 12, 1] 15 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 41, 22, 23, 24, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 31 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517252 none O=C([O-])C1=CC=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 16, 1, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 13, 15, 15, 8, 8, 8, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 15, 15, 15, 15, 8, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15] 15 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 40, 41]) total number of confs: 40 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517252 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517252 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517252/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517252 Building REAL300004517253 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517253' /scratch/stefan/7774842/working/building/REAL300004517253 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517253 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517253/0 /scratch/stefan/7774842/working/building/REAL300004517253 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 287) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/287 `/scratch/stefan/7774842/working/3D/287' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1CC2(C1)CC(C(=O)NC1=CC=C(N3CCCCC3)C=N1)C2) `REAL300004517253.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517253/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517253 none O=C([O-])C1CC2(C1)CC(C(=O)NC1=CC=C(N3CCCCC3)C=N1)C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [35, 21, 35, 21, 21, 21, 21, 21, 3, 3, 3, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 3, 1, 1, 10, 10, 10, 10, 10, 10, 10, 11, 10, 10, 1, 21, 21] 51 rigid atoms, others: [34, 35, 11, 12, 13, 14, 15, 16, 46, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48]) total number of confs: 115 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517253 none O=C([O-])C1CC2(C1)CC(C(=O)NC1=CC=C(N3CCCCC3)C=N1)C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 21, 21, 21, 21, 51, 51, 51, 51, 51, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 21, 21, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 21, 1, 1] 51 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 47, 48, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 95 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517253 none O=C([O-])C1CC2(C1)CC(C(=O)NC1=CC=C(N3CCCCC3)C=N1)C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 51, 51, 51, 51, 51, 21, 21, 21, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 51, 51, 51, 51, 51, 51, 51, 51, 51, 21, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 51, 51] 51 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 46, 47, 48]) total number of confs: 143 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517253 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517253 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517253/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517253 Building REAL300004517254 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517254' /scratch/stefan/7774842/working/building/REAL300004517254 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517254 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517254/0 /scratch/stefan/7774842/working/building/REAL300004517254 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 288) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/288 `/scratch/stefan/7774842/working/3D/288' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)[O-])=NC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=C1) `REAL300004517254.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517254/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517254 none COC1=CC(C(=O)[O-])=NC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 8, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [14, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 1, 1, 9, 14, 14, 14, 9, 3, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 9] 23 rigid atoms, others: [32, 43, 12, 13, 14, 15, 16, 17, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44]) total number of confs: 32 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517254 none COC1=CC(C(=O)[O-])=NC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 8, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 6, 9, 9, 9, 9, 23, 23, 23, 23, 23, 9, 9, 1, 3, 3, 3, 1, 6, 9, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 1] 23 rigid atoms, others: [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 44, 25, 29] set([0, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517254 none COC1=CC(C(=O)[O-])=NC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 8, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 23, 23, 11, 11, 11, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 23, 23, 23, 23, 23, 11, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 23] 23 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 43, 44]) total number of confs: 44 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517254 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517254 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517254/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517254 Building REAL300004517255 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517255' /scratch/stefan/7774842/working/building/REAL300004517255 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517255 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517255/0 /scratch/stefan/7774842/working/building/REAL300004517255 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 289) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/289 `/scratch/stefan/7774842/working/3D/289' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(C(=O)[O-])=CC=C1C(=O)NC1=CC=C(N2CCCCC2)C=N1) `REAL300004517255.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517255/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517255 none CN1C(C(=O)[O-])=CC=C1C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 11, 11, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 17, 17, 17, 17, 17, 3, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1] 22 rigid atoms, others: [42, 11, 12, 13, 14, 15, 16, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 33 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517255 none CN1C(C(=O)[O-])=CC=C1C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 11, 11, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 11, 11, 11, 17, 17, 17, 17, 22, 22, 22, 22, 22, 17, 17, 2, 2, 2, 1, 1, 11, 17, 17, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 17] 22 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 9, 27, 28] set([4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 55 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517255 none CN1C(C(=O)[O-])=CC=C1C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 11, 11, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 12, 12, 12, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 22, 22, 22, 22, 22, 12, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10] 22 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 42]) total number of confs: 35 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517255 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517255 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517255/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517255 Building REAL300004517256 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517256' /scratch/stefan/7774842/working/building/REAL300004517256 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517256 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517256/0 /scratch/stefan/7774842/working/building/REAL300004517256 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 290) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/290 `/scratch/stefan/7774842/working/3D/290' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1(C(=O)NC2=CC=C(N3CCCCC3)C=N2)CC=CC1) `REAL300004517256.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517256.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517256/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517256 none O=C([O-])C1(C(=O)NC2=CC=C(N3CCCCC3)C=N2)CC=CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [15, 9, 15, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 1, 1, 9, 9, 9, 9, 3, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 9, 9, 9, 9, 9, 9] 34 rigid atoms, others: [36, 6, 7, 8, 9, 10, 11, 17, 18, 24, 25] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42]) total number of confs: 53 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517256 none O=C([O-])C1(C(=O)NC2=CC=C(N3CCCCC3)C=N2)CC=CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 5, 5, 5, 9, 9, 9, 9, 34, 34, 34, 34, 34, 9, 9, 1, 1, 1, 1, 5, 9, 9, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 9, 1, 1, 1, 1, 1, 1] 34 rigid atoms, others: [1, 3, 4, 37, 38, 39, 40, 41, 42, 19, 20, 21, 22] set([0, 2, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517256 none O=C([O-])C1(C(=O)NC2=CC=C(N3CCCCC3)C=N2)CC=CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 1, 1, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 13, 13, 13, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 34, 34, 34, 34, 13, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 34, 34, 34, 34, 34, 34] 34 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 97 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517256 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517256 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517256/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517256 Building REAL300004517257 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517257' /scratch/stefan/7774842/working/building/REAL300004517257 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517257 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517257/0 /scratch/stefan/7774842/working/building/REAL300004517257 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 291) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/291 `/scratch/stefan/7774842/working/3D/291' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CCC1=CC=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C1) `REAL300004517257.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517257.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517257/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517257 none O=C([O-])CCC1=CC=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [59, 47, 57, 29, 11, 11, 11, 11, 3, 3, 3, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 11, 11, 47, 47, 29, 29, 11, 11, 3, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 11, 11] 83 rigid atoms, others: [33, 34, 11, 12, 13, 14, 15, 16, 22, 23, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47]) total number of confs: 236 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517257 none O=C([O-])CCC1=CC=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [17, 8, 16, 4, 1, 1, 1, 1, 1, 1, 6, 6, 6, 11, 11, 11, 11, 48, 48, 48, 48, 48, 11, 11, 1, 1, 8, 8, 4, 4, 1, 1, 6, 11, 11, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 11, 1, 1] 83 rigid atoms, others: [4, 5, 6, 7, 8, 9, 46, 47, 24, 25, 30, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517257 none O=C([O-])CCC1=CC=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 82, 62, 48, 48, 48, 48, 20, 20, 20, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 48, 48, 83, 83, 62, 62, 48, 48, 20, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 48, 48] 83 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 45, 46, 47]) total number of confs: 276 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517257 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517257 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517257/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517257 Building REAL300004517258 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517258' /scratch/stefan/7774842/working/building/REAL300004517258 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517258 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517258/0 /scratch/stefan/7774842/working/building/REAL300004517258 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 292) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/292 `/scratch/stefan/7774842/working/3D/292' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=NN1) `REAL300004517258.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517258/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517258 none CC1=C(C(=O)[O-])C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 25, 25, 3, 3, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 1, 1, 17, 17, 17, 17, 17, 3, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 17] 37 rigid atoms, others: [40, 9, 10, 11, 12, 13, 14, 20, 21, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41]) total number of confs: 62 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517258 none CC1=C(C(=O)[O-])C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 13, 13, 13, 17, 17, 17, 17, 37, 37, 37, 37, 37, 17, 17, 1, 1, 2, 2, 2, 13, 17, 17, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 17, 1] 37 rigid atoms, others: [0, 1, 2, 3, 6, 7, 41, 22, 23] set([4, 5, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517258 none CC1=C(C(=O)[O-])C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 37, 37, 12, 12, 12, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 37, 37, 37, 37, 37, 12, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 37] 37 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 13, 14, 15, 16, 17, 18, 19, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 40, 41]) total number of confs: 61 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517258 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517258 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517258/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517258 Building REAL300004517259 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517259' /scratch/stefan/7774842/working/building/REAL300004517259 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517259 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517259/0 /scratch/stefan/7774842/working/building/REAL300004517259 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 293) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/293 `/scratch/stefan/7774842/working/3D/293' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1(CC(=O)NC2=CC=C(N3CCCCC3)C=N2)CC1) `REAL300004517259.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517259/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517259 none O=C([O-])CC1(CC(=O)NC2=CC=C(N3CCCCC3)C=N2)CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [34, 31, 34, 26, 18, 3, 3, 3, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 26, 26, 31, 31, 18, 18, 3, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 26, 26, 26, 26] 45 rigid atoms, others: [8, 9, 10, 11, 12, 13, 40, 19, 20, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44]) total number of confs: 136 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517259 none O=C([O-])CC1(CC(=O)NC2=CC=C(N3CCCCC3)C=N2)CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [10, 5, 10, 1, 1, 1, 6, 19, 19, 19, 26, 26, 26, 26, 45, 45, 45, 45, 45, 26, 26, 1, 1, 5, 5, 6, 6, 19, 26, 26, 45, 45, 45, 45, 45, 45, 45, 45, 45, 45, 26, 1, 1, 1, 1] 45 rigid atoms, others: [3, 4, 5, 41, 42, 43, 44, 21, 22] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517259 none O=C([O-])CC1(CC(=O)NC2=CC=C(N3CCCCC3)C=N2)CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 45 conformations in input total number of sets (complete confs): 45 using default count positions algorithm for smaller data unique positions, atoms: [45, 45, 45, 45, 40, 17, 17, 17, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 45, 45, 45, 45, 40, 40, 17, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 45, 45, 45, 45] 45 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 40, 41, 42, 43, 44]) total number of confs: 152 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517259 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517259 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517259/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517259 Building REAL300004517260 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517260' /scratch/stefan/7774842/working/building/REAL300004517260 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517260 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517260/0 /scratch/stefan/7774842/working/building/REAL300004517260 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 294) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/294 `/scratch/stefan/7774842/working/3D/294' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1C(F)(F)C12CC(C(=O)NC1=CC=C(N3CCCCC3)C=N1)C2) `REAL300004517260.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517260 none O=C([O-])C1C(F)(F)C12CC(C(=O)NC1=CC=C(N3CCCCC3)C=N1)C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 15, 15, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 21, 41, 21, 21, 21, 21, 21, 21, 3, 3, 3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 1, 1, 21, 21, 21, 21, 21, 3, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 21, 21] 50 rigid atoms, others: [32, 43, 12, 13, 14, 15, 16, 17, 23, 24, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45]) total number of confs: 136 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517260 none O=C([O-])C1C(F)(F)C12CC(C(=O)NC1=CC=C(N3CCCCC3)C=N1)C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 15, 15, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 21, 21, 21, 21, 50, 50, 50, 50, 50, 21, 21, 1, 1, 1, 1, 1, 12, 21, 21, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 1, 1] 50 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 44, 45, 25, 26, 27, 28, 29] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 98 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517260 none O=C([O-])C1C(F)(F)C12CC(C(=O)NC1=CC=C(N3CCCCC3)C=N1)C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 15, 15, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50, 50, 50, 50, 14, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 43, 44, 45]) total number of confs: 118 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517260 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517260 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517260/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517260 Building REAL300004517261 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517261' /scratch/stefan/7774842/working/building/REAL300004517261 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517261 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517261/0 /scratch/stefan/7774842/working/building/REAL300004517261 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 295) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/295 `/scratch/stefan/7774842/working/3D/295' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=NC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=CS1) `REAL300004517261.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517261/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517261 none O=C([O-])C1=NC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 1, 1, 8, 8, 3, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 8] 10 rigid atoms, others: [36, 8, 9, 10, 11, 12, 13, 19, 20, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37]) total number of confs: 20 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517261 none O=C([O-])C1=NC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 5, 5, 6, 8, 8, 8, 8, 10, 10, 10, 10, 10, 8, 8, 1, 1, 6, 8, 8, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 8, 1] 10 rigid atoms, others: [1, 3, 4, 5, 6, 21, 22, 37] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 27 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517261 none O=C([O-])C1=NC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 14, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 8, 8, 8, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 10, 10, 8, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 10] 10 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 37, 36]) total number of confs: 19 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517261 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517261 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517261/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517261 Building REAL300004517262 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517262' /scratch/stefan/7774842/working/building/REAL300004517262 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517262 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517262/0 /scratch/stefan/7774842/working/building/REAL300004517262 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 296) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/296 `/scratch/stefan/7774842/working/3D/296' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]1(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C[C@H]1C(=O)[O-]) `REAL300004517262.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517262/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517262 none C[C@]1(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C[C@H]1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 5, 7, 1, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 1, 1, 7, 7, 7, 7, 9, 9, 7, 7, 7, 3, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 7, 7] 16 rigid atoms, others: [4, 5, 6, 7, 8, 9, 39, 15, 16, 27, 28] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41]) total number of confs: 33 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517262 none C[C@]1(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C[C@H]1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 5, 7, 1, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 4, 4, 4, 7, 7, 7, 7, 16, 16, 16, 16, 16, 7, 7, 1, 1, 1, 1, 3, 3, 2, 2, 2, 4, 7, 7, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 7, 1, 1] 16 rigid atoms, others: [0, 1, 2, 40, 41, 17, 18, 19, 20] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517262 none C[C@]1(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C[C@H]1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 5, 7, 1, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [16, 10, 10, 10, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 16, 16, 16, 16, 16, 16, 16, 16, 16, 10, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 16, 16] 16 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 39, 40, 41]) total number of confs: 43 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517262 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517262 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517262/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517262 Building REAL300004517263 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517263' /scratch/stefan/7774842/working/building/REAL300004517263 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517263 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517263/0 /scratch/stefan/7774842/working/building/REAL300004517263 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 297) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/297 `/scratch/stefan/7774842/working/3D/297' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C(C(=O)[O-])S1) `REAL300004517263.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517263.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517263/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517263 none CC1=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 1, 11, 11, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 3, 3, 3, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 3, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 16] 25 rigid atoms, others: [5, 6, 7, 8, 9, 10, 16, 17, 40, 28, 29] set([0, 1, 2, 3, 4, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41]) total number of confs: 32 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517263 none CC1=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 1, 11, 11, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 9, 9, 9, 16, 16, 16, 16, 25, 25, 25, 25, 25, 16, 16, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 16, 16, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 16, 1] 25 rigid atoms, others: [0, 1, 2, 3, 41, 18, 19, 20, 21, 22, 23] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 57 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517263 none CC1=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 1, 11, 11, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 14, 14, 14, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 25, 25, 25, 25, 25, 25, 25, 25, 25, 14, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 25] 25 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 9, 10, 11, 12, 13, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 40, 41]) total number of confs: 46 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517263 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517263 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517263/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517263 Building REAL300004517264 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517264' /scratch/stefan/7774842/working/building/REAL300004517264 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517264 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517264/0 /scratch/stefan/7774842/working/building/REAL300004517264 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 298) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/298 `/scratch/stefan/7774842/working/3D/298' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=C(S1)SC(C(=O)NC1=CC=C(N3CCCCC3)C=N1)=C2) `REAL300004517264.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517264.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517264/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517264 none O=C([O-])C1=CC2=C(S1)SC(C(=O)NC1=CC=C(N3CCCCC3)C=N1)=C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 14, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 1, 1, 18, 18, 3, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 18] 20 rigid atoms, others: [40, 12, 13, 14, 15, 16, 17, 23, 24, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41]) total number of confs: 31 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517264 none O=C([O-])C1=CC2=C(S1)SC(C(=O)NC1=CC=C(N3CCCCC3)C=N1)=C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 14, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 18, 18, 18, 18, 20, 20, 20, 20, 20, 18, 18, 1, 1, 12, 18, 18, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 18, 1] 20 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 41, 25, 26] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517264 none O=C([O-])C1=CC2=C(S1)SC(C(=O)NC1=CC=C(N3CCCCC3)C=N1)=C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 14, 14, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 20, 20, 10, 10, 10, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 20, 20, 10, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 20] 20 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 40, 41]) total number of confs: 35 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517264 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517264 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517264/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517264 Building REAL300004517265 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517265' /scratch/stefan/7774842/working/building/REAL300004517265 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517265 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517265/0 /scratch/stefan/7774842/working/building/REAL300004517265 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 299) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/299 `/scratch/stefan/7774842/working/3D/299' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)[O-])=C(Cl)C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=C1) `REAL300004517265.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517265.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517265/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517265 none COC1=CC(C(=O)[O-])=C(Cl)C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 16, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [23, 13, 13, 13, 13, 13, 23, 23, 13, 13, 3, 3, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 1, 1, 13, 23, 23, 23, 13, 3, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 13] 44 rigid atoms, others: [32, 33, 44, 13, 14, 15, 16, 17, 18, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45]) total number of confs: 86 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517265 none COC1=CC(C(=O)[O-])=C(Cl)C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 16, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 7, 7, 7, 13, 13, 13, 13, 30, 30, 30, 30, 30, 13, 13, 1, 3, 3, 3, 1, 7, 13, 13, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 13, 1] 44 rigid atoms, others: [1, 2, 3, 4, 5, 8, 9, 10, 11, 45, 26, 30] set([0, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517265 none COC1=CC(C(=O)[O-])=C(Cl)C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 16, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [44, 30, 30, 30, 30, 30, 44, 44, 30, 30, 10, 10, 10, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 30, 44, 44, 44, 30, 10, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 30] 44 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 44, 45]) total number of confs: 130 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517265 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517265 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517265/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517265 Building REAL300004517266 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517266' /scratch/stefan/7774842/working/building/REAL300004517266 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517266 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517266/0 /scratch/stefan/7774842/working/building/REAL300004517266 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 300) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/300 `/scratch/stefan/7774842/working/3D/300' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=CC(F)=C1C(=O)NC1=CC=C(N2CCCCC2)C=N1) `REAL300004517266.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517266/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517266 none CC1=C(C(=O)[O-])C=CC(F)=C1C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 15, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 1, 1, 18, 18, 18, 18, 18, 3, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1] 25 rigid atoms, others: [32, 33, 44, 13, 14, 15, 16, 17, 18, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 33 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517266 none CC1=C(C(=O)[O-])C=CC(F)=C1C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 15, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 18, 18, 18, 18, 25, 25, 25, 25, 25, 18, 18, 2, 2, 2, 1, 1, 10, 18, 18, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 18] 25 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 9, 10, 11, 29, 30] set([4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 59 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517266 none CC1=C(C(=O)[O-])C=CC(F)=C1C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 15, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 13, 13, 13, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 9, 9, 25, 25, 25, 25, 25, 13, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9] 25 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 44]) total number of confs: 44 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517266 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517266 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517266/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517266 Building REAL300004517267 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517267' /scratch/stefan/7774842/working/building/REAL300004517267 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517267 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517267/0 /scratch/stefan/7774842/working/building/REAL300004517267 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 301) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/301 `/scratch/stefan/7774842/working/3D/301' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C2C=C(C(=O)NC3=CC=C(N4CCCCC4)C=N3)SC2=CC=C1) `REAL300004517267.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517267.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517267/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517267 none O=C([O-])C1=C2C=C(C(=O)NC3=CC=C(N4CCCCC4)C=N3)SC2=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 14, 1, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [37, 21, 37, 21, 21, 21, 3, 3, 3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 1, 1, 21, 21, 21, 21, 21, 21, 3, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 21, 21, 21] 39 rigid atoms, others: [9, 10, 11, 12, 13, 14, 20, 21, 41, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44]) total number of confs: 100 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517267 none O=C([O-])C1=C2C=C(C(=O)NC3=CC=C(N4CCCCC4)C=N3)SC2=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 14, 1, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 12, 12, 13, 21, 21, 21, 21, 39, 39, 39, 39, 39, 21, 21, 1, 1, 1, 1, 1, 1, 13, 21, 21, 39, 39, 39, 39, 39, 39, 39, 39, 39, 39, 21, 1, 1, 1] 39 rigid atoms, others: [1, 3, 4, 5, 6, 7, 42, 43, 44, 22, 23, 24, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517267 none O=C([O-])C1=C2C=C(C(=O)NC3=CC=C(N4CCCCC4)C=N3)SC2=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 14, 1, 1, 1, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 39 conformations in input total number of sets (complete confs): 39 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 39, 39, 39, 11, 11, 11, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 9, 9, 39, 39, 39, 39, 39, 39, 11, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 39, 39, 39] 39 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 41, 42, 43, 44]) total number of confs: 54 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517267 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517267 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517267/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517267 Building REAL300004517268 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517268' /scratch/stefan/7774842/working/building/REAL300004517268 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517268 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517268/0 /scratch/stefan/7774842/working/building/REAL300004517268 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 302) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/302 `/scratch/stefan/7774842/working/3D/302' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=NC=CC=C1CCC(=O)NC1=CC=C(N2CCCCC2)C=N1) `REAL300004517268.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517268.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517268/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517268 none O=C([O-])C1=NC=CC=C1CCC(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 1, 1, 1, 1, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 14, 14, 3, 3, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 1, 1, 21, 21, 21, 14, 14, 14, 14, 3, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1] 21 rigid atoms, others: [34, 35, 13, 14, 15, 16, 17, 18, 46, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 61 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517268 none O=C([O-])C1=NC=CC=C1CCC(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 1, 1, 1, 1, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 5, 7, 17, 17, 17, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 5, 5, 7, 7, 17, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21] 21 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 26, 27, 28] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 66 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517268 none O=C([O-])C1=NC=CC=C1CCC(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 1, 1, 1, 1, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 21, 18, 18, 6, 6, 6, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 4, 4, 21, 21, 21, 18, 18, 18, 18, 6, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4] 21 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 46]) total number of confs: 67 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517268 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517268 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517268/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517268 Building REAL300004517269 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517269' /scratch/stefan/7774842/working/building/REAL300004517269 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517269 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517269/0 /scratch/stefan/7774842/working/building/REAL300004517269 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 303) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/303 `/scratch/stefan/7774842/working/3D/303' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C12CC(C(=O)NC3=CC=C(N4CCCCC4)C=N3)(C1)OC2) `REAL300004517269.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517269.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517269/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517269 none O=C([O-])C12CC(C(=O)NC3=CC=C(N4CCCCC4)C=N3)(C1)OC2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 12, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [33, 20, 33, 20, 20, 3, 3, 3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 1, 1, 20, 20, 20, 20, 20, 3, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 20, 20, 20, 20] 43 rigid atoms, others: [39, 8, 9, 10, 11, 12, 13, 19, 20, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43]) total number of confs: 87 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517269 none O=C([O-])C12CC(C(=O)NC3=CC=C(N4CCCCC4)C=N3)(C1)OC2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 12, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 13, 13, 13, 20, 20, 20, 20, 43, 43, 43, 43, 43, 20, 20, 1, 1, 1, 1, 1, 13, 20, 20, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 20, 1, 1, 1, 1] 43 rigid atoms, others: [1, 3, 4, 5, 6, 40, 41, 42, 43, 21, 22, 23, 24, 25] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517269 none O=C([O-])C12CC(C(=O)NC3=CC=C(N4CCCCC4)C=N3)(C1)OC2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 12, 5, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 43, 16, 16, 16, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 9, 9, 43, 43, 43, 43, 43, 16, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 43, 43, 43, 43] 43 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 39, 40, 41, 42, 43]) total number of confs: 71 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517269 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517269 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517269/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517269 Building REAL300004517270 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517270' /scratch/stefan/7774842/working/building/REAL300004517270 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517270 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517270/0 /scratch/stefan/7774842/working/building/REAL300004517270 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 304) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/304 `/scratch/stefan/7774842/working/3D/304' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(/C=C/C(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C1) `REAL300004517270.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517270.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517270/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517270 none O=C([O-])C1=CC=C(/C=C/C(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [26, 20, 26, 20, 26, 26, 20, 20, 3, 3, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 1, 1, 26, 26, 26, 26, 20, 20, 3, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 26, 26] 27 rigid atoms, others: [32, 43, 11, 12, 13, 14, 15, 16, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45]) total number of confs: 106 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517270 none O=C([O-])C1=CC=C(/C=C/C(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 3, 3, 17, 17, 17, 26, 26, 26, 26, 27, 27, 27, 27, 27, 26, 26, 1, 1, 1, 1, 3, 3, 17, 26, 26, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 26, 1, 1] 27 rigid atoms, others: [1, 3, 4, 5, 6, 7, 44, 45, 24, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 63 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517270 none O=C([O-])C1=CC=C(/C=C/C(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 27, 27, 27, 27, 27, 10, 10, 10, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 27, 27, 27, 27, 27, 27, 10, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 27, 27] 27 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 43, 44, 45]) total number of confs: 70 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517270 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517270 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517270/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517270 Building REAL300004517271 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517271' /scratch/stefan/7774842/working/building/REAL300004517271 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517271 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517271/0 /scratch/stefan/7774842/working/building/REAL300004517271 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 305) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/305 `/scratch/stefan/7774842/working/3D/305' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1CC1(C(=O)[O-])C(=O)NC1=CC=C(N2CCCCC2)C=N1) `REAL300004517271.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517271.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517271/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517271 none CC1CC1(C(=O)[O-])C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 3, 8, 10, 10, 3, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 1, 1, 8, 8, 8, 8, 8, 8, 3, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1] 19 rigid atoms, others: [9, 10, 11, 12, 13, 14, 20, 21, 41, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 37 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517271 none CC1CC1(C(=O)[O-])C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 3, 3, 1, 4, 4, 5, 8, 8, 8, 8, 19, 19, 19, 19, 19, 8, 8, 2, 2, 2, 1, 1, 1, 5, 8, 8, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 8] 19 rigid atoms, others: [0, 1, 2, 3, 4, 7, 25, 26, 27] set([5, 6, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 49 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517271 none CC1CC1(C(=O)[O-])C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 10, 19, 19, 19, 10, 10, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 19, 19, 19, 19, 19, 19, 10, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8] 19 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 41]) total number of confs: 47 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517271 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517271 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517271/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517271 Building REAL300004517272 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517272' /scratch/stefan/7774842/working/building/REAL300004517272 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517272 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517272/0 /scratch/stefan/7774842/working/building/REAL300004517272 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 306) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/306 `/scratch/stefan/7774842/working/3D/306' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1(C(=O)NC2=CC=C(N3CCCCC3)C=N2)CC2(CCC2)C1) `REAL300004517272.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517272.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517272/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517272 none O=C([O-])C1(C(=O)NC2=CC=C(N3CCCCC3)C=N2)CC2(CCC2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [14, 8, 14, 3, 3, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 1, 1, 8, 8, 8, 8, 8, 8, 3, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8] 26 rigid atoms, others: [38, 6, 7, 8, 9, 10, 11, 17, 18, 26, 27] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 52 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517272 none O=C([O-])C1(C(=O)NC2=CC=C(N3CCCCC3)C=N2)CC2(CCC2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 5, 5, 5, 8, 8, 8, 8, 26, 26, 26, 26, 26, 8, 8, 1, 1, 1, 1, 1, 1, 5, 8, 8, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 26 rigid atoms, others: [1, 3, 4, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 20, 21, 22, 23, 24] set([0, 2, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517272 none O=C([O-])C1(C(=O)NC2=CC=C(N3CCCCC3)C=N2)CC2(CCC2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 13, 13, 13, 6, 6, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 26, 26, 26, 26, 26, 26, 13, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26] 26 rigid atoms, others: [32, 33, 34, 35, 36, 37, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 77 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517272 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517272 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517272/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517272 Building REAL300004517273 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517273' /scratch/stefan/7774842/working/building/REAL300004517273 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517273 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517273/0 /scratch/stefan/7774842/working/building/REAL300004517273 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 307) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/307 `/scratch/stefan/7774842/working/3D/307' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=CC(C(=O)[O-])=C1C(=O)NC1=CC=C(N2CCCCC2)C=N1) `REAL300004517273.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517273.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517273/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517273 none CN1N=CC(C(=O)[O-])=C1C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 11, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 17, 17, 3, 3, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 1, 1, 11, 11, 11, 11, 3, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1] 32 rigid atoms, others: [41, 11, 12, 13, 14, 15, 16, 22, 23, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 48 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517273 none CN1N=CC(C(=O)[O-])=C1C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 11, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 8, 8, 8, 11, 11, 11, 11, 32, 32, 32, 32, 32, 11, 11, 2, 2, 2, 1, 8, 11, 11, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 11] 32 rigid atoms, others: [0, 1, 2, 3, 4, 5, 8, 9, 27] set([6, 7, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 64 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517273 none CN1N=CC(C(=O)[O-])=C1C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 1, 11, 11, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [32, 32, 32, 32, 32, 32, 32, 32, 13, 13, 13, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 32, 32, 32, 32, 13, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7] 32 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 41]) total number of confs: 58 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517273 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517273 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517273/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517273 Building REAL300004517274 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517274' /scratch/stefan/7774842/working/building/REAL300004517274 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517274 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517274/0 /scratch/stefan/7774842/working/building/REAL300004517274 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 308) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/308 `/scratch/stefan/7774842/working/3D/308' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CSC2=C1NC(C(=O)NC1=CC=C(N3CCCCC3)C=N1)=C2) `REAL300004517274.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517274/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517274 none O=C([O-])C1=CSC2=C1NC(C(=O)NC1=CC=C(N3CCCCC3)C=N1)=C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 1, 8, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [31, 22, 31, 22, 22, 22, 22, 22, 22, 3, 3, 3, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 22, 22, 22, 3, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 22] 34 rigid atoms, others: [41, 12, 13, 14, 15, 16, 17, 23, 24, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42]) total number of confs: 74 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517274 none O=C([O-])C1=CSC2=C1NC(C(=O)NC1=CC=C(N3CCCCC3)C=N1)=C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 1, 8, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 22, 22, 22, 22, 34, 34, 34, 34, 34, 22, 22, 1, 1, 1, 13, 22, 22, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 22, 1] 34 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27, 42] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517274 none O=C([O-])C1=CSC2=C1NC(C(=O)NC1=CC=C(N3CCCCC3)C=N1)=C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 1, 8, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 34, 34, 34, 34, 34, 12, 12, 12, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 34, 34, 34, 12, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 34] 34 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 41, 42]) total number of confs: 49 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517274 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517274 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517274/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517274 Building REAL300004517275 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517275' /scratch/stefan/7774842/working/building/REAL300004517275 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517275 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517275/0 /scratch/stefan/7774842/working/building/REAL300004517275 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 309) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/309 `/scratch/stefan/7774842/working/3D/309' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=C(C=C(C(=O)NC3=CC=C(N4CCCCC4)C=N3)N2)S1) `REAL300004517275.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517275 none O=C([O-])C1=CC2=C(C=C(C(=O)NC3=CC=C(N4CCCCC4)C=N3)N2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 8, 14, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 3, 3, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 1, 1, 17, 17, 17, 17, 3, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 17] 18 rigid atoms, others: [41, 11, 12, 13, 14, 15, 16, 22, 23, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42]) total number of confs: 30 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517275 none O=C([O-])C1=CC2=C(C=C(C(=O)NC3=CC=C(N4CCCCC4)C=N3)N2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 8, 14, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 10, 10, 11, 17, 17, 17, 17, 18, 18, 18, 18, 18, 17, 17, 1, 1, 1, 1, 11, 17, 17, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 17, 1] 18 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 42, 24, 25, 26, 27] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) 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.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517275 none O=C([O-])C1=CC2=C(C=C(C(=O)NC3=CC=C(N4CCCCC4)C=N3)N2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 8, 14, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 18, 10, 10, 10, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 18, 18, 18, 18, 10, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 18] 18 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 41, 42]) total number of confs: 32 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517275 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517275 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517275/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517275 Building REAL300004517276 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517276' /scratch/stefan/7774842/working/building/REAL300004517276 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517276 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517276/0 /scratch/stefan/7774842/working/building/REAL300004517276 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 310) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/310 `/scratch/stefan/7774842/working/3D/310' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=COC2=C1NC(C(=O)NC1=CC=C(N3CCCCC3)C=N1)=C2) `REAL300004517276.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517276 none O=C([O-])C1=COC2=C1NC(C(=O)NC1=CC=C(N3CCCCC3)C=N1)=C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 12, 1, 1, 8, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [31, 23, 31, 23, 23, 23, 23, 23, 23, 3, 3, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 1, 1, 23, 23, 23, 3, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 23] 33 rigid atoms, others: [41, 12, 13, 14, 15, 16, 17, 23, 24, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42]) total number of confs: 69 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517276 none O=C([O-])C1=COC2=C1NC(C(=O)NC1=CC=C(N3CCCCC3)C=N1)=C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 12, 1, 1, 8, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 13, 23, 23, 23, 23, 33, 33, 33, 33, 33, 23, 23, 1, 1, 1, 13, 23, 23, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 23, 1] 33 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27, 42] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 74 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517276 none O=C([O-])C1=COC2=C1NC(C(=O)NC1=CC=C(N3CCCCC3)C=N1)=C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 12, 1, 1, 8, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 33, 33, 33, 33, 11, 11, 11, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 33, 33, 33, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 33] 33 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 16, 17, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 41, 42]) total number of confs: 52 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517276 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517276 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517276/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517276 Building REAL300004517277 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517277' /scratch/stefan/7774842/working/building/REAL300004517277 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517277 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517277/0 /scratch/stefan/7774842/working/building/REAL300004517277 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 311) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/311 `/scratch/stefan/7774842/working/3D/311' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=CC=C1C(=O)NC1=CC=C(N2CCCCC2)C=N1) `REAL300004517277.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517277.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517277/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517277 none CC1=C(C(=O)[O-])C=CC=C1C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 16, 16, 3, 3, 3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 1, 1, 16, 16, 16, 16, 16, 16, 3, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1] 22 rigid atoms, others: [32, 33, 44, 12, 13, 14, 15, 16, 17, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 31 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517277 none CC1=C(C(=O)[O-])C=CC=C1C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 10, 10, 10, 16, 16, 16, 16, 22, 22, 22, 22, 22, 16, 16, 2, 2, 2, 1, 1, 1, 10, 16, 16, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 16] 22 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 9, 10, 28, 29, 30] set([4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517277 none CC1=C(C(=O)[O-])C=CC=C1C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 22, 22, 13, 13, 13, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 9, 9, 22, 22, 22, 22, 22, 22, 13, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9] 22 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 44]) total number of confs: 41 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517277 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517277 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517277/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517277 Building REAL300004517278 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517278' /scratch/stefan/7774842/working/building/REAL300004517278 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517278 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517278/0 /scratch/stefan/7774842/working/building/REAL300004517278 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 312) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/312 `/scratch/stefan/7774842/working/3D/312' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=CC(=O)NC2=CC=C(N3CCCCC3)C=N2)C=N1) `REAL300004517278.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517278.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517278/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517278 none O=C([O-])C1=CC=C(C=CC(=O)NC2=CC=C(N3CCCCC3)C=N2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 48, 20, 20, 3, 3, 3, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 48, 48, 48, 48, 21, 21, 3, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 48] 50 rigid atoms, others: [32, 43, 11, 12, 13, 14, 15, 16, 22, 23, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44]) total number of confs: 101 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517278 none O=C([O-])C1=CC=C(C=CC(=O)NC2=CC=C(N3CCCCC3)C=N2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 5, 5, 29, 29, 29, 48, 48, 48, 48, 50, 50, 50, 50, 50, 48, 48, 1, 1, 1, 1, 5, 5, 29, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 1] 50 rigid atoms, others: [1, 3, 4, 5, 6, 7, 44, 24, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 113 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517278 none O=C([O-])C1=CC=C(C=CC(=O)NC2=CC=C(N3CCCCC3)C=N2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 41, 41, 14, 14, 14, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50, 50, 50, 50, 41, 41, 14, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 43, 44]) total number of confs: 119 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517278 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517278 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517278/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517278 Building REAL300004517279 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517279' /scratch/stefan/7774842/working/building/REAL300004517279 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517279 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517279/0 /scratch/stefan/7774842/working/building/REAL300004517279 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 313) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/313 `/scratch/stefan/7774842/working/3D/313' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CCC1(C(=O)[O-])C(=O)NC1=CC=C(N2CCCCC2)C=N1) `REAL300004517279.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517279.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517279/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517279 none C=C1CCC1(C(=O)[O-])C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 3, 8, 14, 14, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 1, 1, 8, 8, 8, 8, 8, 8, 3, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1] 25 rigid atoms, others: [10, 11, 12, 13, 14, 15, 21, 22, 42, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 51 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517279 none C=C1CCC1(C(=O)[O-])C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 1, 5, 5, 5, 8, 8, 8, 8, 25, 25, 25, 25, 25, 8, 8, 1, 1, 1, 1, 1, 1, 5, 8, 8, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8] 25 rigid atoms, others: [0, 1, 2, 3, 4, 5, 8, 23, 24, 25, 26, 27, 28] set([6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 46 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517279 none C=C1CCC1(C(=O)[O-])C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 11, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 13, 25, 25, 25, 13, 13, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 25, 25, 25, 25, 25, 25, 13, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6] 25 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 42]) total number of confs: 71 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517279 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517279 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517279/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517279 Building REAL300004517280 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517280' /scratch/stefan/7774842/working/building/REAL300004517280 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517280 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517280/0 /scratch/stefan/7774842/working/building/REAL300004517280 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 314) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/314 `/scratch/stefan/7774842/working/3D/314' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CSC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=C1) `REAL300004517280.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517280.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517280/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517280 none O=C([O-])C1=CSC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 3, 3, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 1, 1, 22, 22, 3, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 22] 29 rigid atoms, others: [37, 9, 10, 11, 12, 13, 14, 20, 21, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38]) total number of confs: 35 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517280 none O=C([O-])C1=CSC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 22, 22, 22, 22, 29, 29, 29, 29, 29, 22, 22, 1, 1, 13, 22, 22, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 22, 1] 29 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 22, 23, 38] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517280 none O=C([O-])C1=CSC(C(=O)NC2=CC=C(N3CCCCC3)C=N2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 29, 29, 11, 11, 11, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 7, 7, 29, 29, 11, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 29] 29 rigid atoms, others: [32, 33, 34, 35, 36, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 37, 38]) total number of confs: 52 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517280 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517280 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517280/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517280 Building REAL300004517281 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517281' /scratch/stefan/7774842/working/building/REAL300004517281 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517281 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517281/0 /scratch/stefan/7774842/working/building/REAL300004517281 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 315) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/315 `/scratch/stefan/7774842/working/3D/315' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])[C@H]1[C@@H]2CC[C@@H](O2)[C@H]1C(=O)NC1=CC=C(N2CCCCC2)C=N1) `REAL300004517281.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517281.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517281/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517281 none O=C([O-])[C@H]1[C@@H]2CC[C@@H](O2)[C@H]1C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 7, 5, 5, 5, 7, 12, 5, 7, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 6, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 1, 1, 6, 6, 6, 6, 3, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1] 10 rigid atoms, others: [34, 35, 46, 16, 17, 18, 19, 20, 21, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 23 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517281 none O=C([O-])[C@H]1[C@@H]2CC[C@@H](O2)[C@H]1C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 7, 5, 5, 5, 7, 12, 5, 7, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 6, 6, 6, 6, 10, 10, 10, 10, 10, 6, 6, 1, 1, 1, 1, 4, 6, 6, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6] 10 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 29, 30, 31] set([0, 2, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 23 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517281 none O=C([O-])[C@H]1[C@@H]2CC[C@@H](O2)[C@H]1C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 7, 5, 5, 5, 7, 12, 5, 7, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 9, 10, 9, 9, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 10, 10, 10, 10, 9, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6] 10 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 46]) total number of confs: 23 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517281 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517281 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517281/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517281 Building REAL300004517282 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517282' /scratch/stefan/7774842/working/building/REAL300004517282 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517282 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517282/0 /scratch/stefan/7774842/working/building/REAL300004517282 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 316) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/316 `/scratch/stefan/7774842/working/3D/316' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC2=C(C(=O)NC3=CC=C(N4CCCCC4)C=N3)C=CC=C12) `REAL300004517282.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517282/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517282 none O=C([O-])C1=CC=CC2=C(C(=O)NC3=CC=C(N4CCCCC4)C=N3)C=CC=C12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [25, 17, 25, 17, 17, 17, 17, 17, 3, 3, 3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 1, 1, 17, 17, 17, 17, 17, 17, 17, 3, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 17, 17, 17] 30 rigid atoms, others: [32, 33, 44, 11, 12, 13, 14, 15, 16, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47]) total number of confs: 64 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517282 none O=C([O-])C1=CC=CC2=C(C(=O)NC3=CC=C(N4CCCCC4)C=N3)C=CC=C12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 17, 17, 17, 17, 30, 30, 30, 30, 30, 17, 17, 1, 1, 1, 1, 1, 1, 1, 9, 17, 17, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 17, 1, 1, 1] 30 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 45, 46, 47, 24, 25, 26, 27, 28, 29, 30] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 63 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517282 none O=C([O-])C1=CC=CC2=C(C(=O)NC3=CC=C(N4CCCCC4)C=N3)C=CC=C12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [30, 30, 30, 30, 30, 30, 30, 30, 14, 14, 14, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 9, 9, 30, 30, 30, 30, 30, 30, 30, 14, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 30, 30, 30] 30 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 44, 45, 46, 47]) total number of confs: 53 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517282 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517282 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517282/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517282 Building REAL300004517283 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517283' /scratch/stefan/7774842/working/building/REAL300004517283 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517283 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517283/0 /scratch/stefan/7774842/working/building/REAL300004517283 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 317) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/317 `/scratch/stefan/7774842/working/3D/317' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@]1(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C[C@H]1C(=O)[O-]) `REAL300004517283.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517283 none CC(C)[C@]1(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C[C@H]1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 5, 7, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [16, 7, 16, 3, 3, 3, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 1, 1, 7, 7, 7, 7, 10, 10, 16, 16, 16, 16, 16, 16, 16, 3, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 7, 7] 33 rigid atoms, others: [33, 34, 6, 7, 8, 9, 10, 11, 45, 17, 18] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47]) total number of confs: 82 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517283 none CC(C)[C@]1(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C[C@H]1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 5, 7, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [6, 1, 6, 1, 1, 4, 4, 4, 7, 7, 7, 7, 27, 27, 27, 27, 27, 7, 7, 1, 1, 1, 1, 3, 3, 6, 6, 6, 6, 6, 6, 6, 4, 7, 7, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 7, 1, 1] 33 rigid atoms, others: [1, 3, 4, 46, 47, 19, 20, 21, 22] set([0, 2, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 64 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517283 none CC(C)[C@]1(C(=O)NC2=CC=C(N3CCCCC3)C=N2)C[C@H]1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 5, 7, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 27, 33, 17, 17, 17, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 9, 9, 27, 27, 27, 27, 31, 31, 33, 33, 33, 33, 33, 33, 33, 17, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 27, 27] 33 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 10, 11, 12, 13, 14, 15, 16, 43, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 45, 46, 47]) total number of confs: 120 number of broken/clashed sets: 7 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517283 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517283 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517283/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517283 Building REAL300004517284 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517284' /scratch/stefan/7774842/working/building/REAL300004517284 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517284 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517284/0 /scratch/stefan/7774842/working/building/REAL300004517284 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 318) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/318 `/scratch/stefan/7774842/working/3D/318' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1CC(=O)NC1=CC=C(N2CCCCC2)C=N1) `REAL300004517284.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517284.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517284/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517284 none CC1=CC(C(=O)[O-])=CC=C1CC(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [62, 62, 62, 31, 62, 62, 62, 62, 62, 24, 3, 3, 3, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 62, 62, 62, 62, 62, 62, 24, 24, 3, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1] 96 rigid atoms, others: [35, 36, 13, 14, 15, 16, 17, 18, 24, 25, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 251 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517284 none CC1=CC(C(=O)[O-])=CC=C1CC(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 36, 36, 36, 62, 62, 62, 62, 96, 96, 96, 96, 96, 62, 62, 2, 2, 2, 1, 1, 1, 6, 6, 36, 62, 62, 96, 96, 96, 96, 96, 96, 96, 96, 96, 96, 62] 96 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 29, 30, 31] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 206 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517284 none CC1=CC(C(=O)[O-])=CC=C1CC(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [96, 96, 96, 79, 96, 96, 96, 96, 96, 77, 20, 20, 20, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 96, 96, 96, 96, 96, 96, 77, 77, 20, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10] 96 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 47]) total number of confs: 374 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517284 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517284 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517284/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517284 Building REAL300004517285 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517285' /scratch/stefan/7774842/working/building/REAL300004517285 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517285 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517285/0 /scratch/stefan/7774842/working/building/REAL300004517285 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 319) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/319 `/scratch/stefan/7774842/working/3D/319' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CSC(CC(=O)NC2=CC=C(N3CCCCC3)C=N2)=C1) `REAL300004517285.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517285.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517285/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517285 none O=C([O-])C1=CSC(CC(=O)NC2=CC=C(N3CCCCC3)C=N2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 103, 103, 103, 103, 22, 3, 3, 3, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 1, 1, 103, 103, 22, 22, 3, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 103] 167 rigid atoms, others: [40, 10, 11, 12, 13, 14, 15, 21, 22, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41]) total number of confs: 181 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517285 none O=C([O-])C1=CSC(CC(=O)NC2=CC=C(N3CCCCC3)C=N2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 58, 58, 58, 103, 103, 103, 103, 167, 167, 167, 167, 167, 103, 103, 1, 1, 9, 9, 58, 103, 103, 167, 167, 167, 167, 167, 167, 167, 167, 167, 167, 103, 1] 167 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 41, 23, 24] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 348 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517285 none O=C([O-])C1=CSC(CC(=O)NC2=CC=C(N3CCCCC3)C=N2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 167 conformations in input total number of sets (complete confs): 167 using faster count positions algorithm for large data unique positions, atoms: [167, 167, 167, 167, 167, 167, 88, 21, 21, 21, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 10, 10, 167, 167, 88, 88, 21, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 167] 167 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 40, 41]) total number of confs: 436 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517285 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517285 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517285/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517285 Building REAL300004517286 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517286' /scratch/stefan/7774842/working/building/REAL300004517286 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517286 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517286/0 /scratch/stefan/7774842/working/building/REAL300004517286 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 320) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/320 `/scratch/stefan/7774842/working/3D/320' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(CC(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C1F) `REAL300004517286.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517286/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517286 none O=C([O-])C1=CC=C(CC(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [69, 37, 69, 37, 37, 37, 9, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 1, 1, 37, 37, 37, 37, 37, 9, 9, 3, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 37] 147 rigid atoms, others: [32, 43, 10, 11, 12, 13, 14, 15, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44]) total number of confs: 201 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517286 none O=C([O-])C1=CC=C(CC(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 7, 21, 21, 21, 37, 37, 37, 37, 147, 147, 147, 147, 147, 37, 37, 1, 1, 1, 1, 1, 7, 7, 21, 37, 37, 147, 147, 147, 147, 147, 147, 147, 147, 147, 147, 37, 1] 147 rigid atoms, others: [1, 3, 4, 5, 6, 7, 44, 23, 24, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 242 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517286 none O=C([O-])C1=CC=C(CC(=O)NC2=CC=C(N3CCCCC3)C=N2)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 1, 1, 15, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [147, 147, 147, 147, 147, 147, 46, 13, 13, 13, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 147, 147, 147, 147, 147, 46, 46, 13, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 147] 147 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 43, 44]) total number of confs: 311 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517286 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517286 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517286/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517286 Building REAL300004517287 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517287' /scratch/stefan/7774842/working/building/REAL300004517287 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517287 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517287/0 /scratch/stefan/7774842/working/building/REAL300004517287 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 321) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/321 `/scratch/stefan/7774842/working/3D/321' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)[C@H](C(=O)[O-])[C@@H]1C(=O)NC1=CC=C(N2CCCCC2)C=N1) `REAL300004517287.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517287.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517287/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517287 none CC1(C)[C@H](C(=O)[O-])[C@@H]1C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 11, 5, 7, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 4, 3, 4, 3, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 1, 1, 4, 4, 4, 4, 4, 4, 3, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1] 6 rigid atoms, others: [32, 33, 44, 12, 13, 14, 15, 16, 17, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 16 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517287 none CC1(C)[C@H](C(=O)[O-])[C@@H]1C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 11, 5, 7, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 3, 3, 3, 4, 4, 4, 4, 6, 6, 6, 6, 6, 4, 4, 2, 2, 2, 2, 2, 2, 3, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4] 6 rigid atoms, others: [0, 1, 2, 3, 4, 5, 8, 9, 10] set([6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 28 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517287 none CC1(C)[C@H](C(=O)[O-])[C@@H]1C(=O)NC1=CC=C(N2CCCCC2)C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 11, 5, 7, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 6, 6, 6, 6, 6, 6, 6, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5] 6 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 44]) total number of confs: 10 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517287 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517287 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517287/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517287 Building REAL300004517288 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517288' /scratch/stefan/7774842/working/building/REAL300004517288 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517288 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517288/0 /scratch/stefan/7774842/working/building/REAL300004517288 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 322) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/322 `/scratch/stefan/7774842/working/3D/322' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C2CCCCC2=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)S1) `REAL300004517288.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517288 none O=C([O-])C1=C2CCCCC2=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 5, 5, 5, 5, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [33, 20, 33, 20, 20, 20, 20, 20, 20, 20, 3, 3, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 3, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1] 35 rigid atoms, others: [48, 36, 37, 13, 14, 15, 16, 17, 18, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 86 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517288 none O=C([O-])C1=C2CCCCC2=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 5, 5, 5, 5, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 11, 20, 20, 20, 20, 35, 35, 35, 35, 35, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 20, 20, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 20] 35 rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 33, 26, 27, 28, 29, 30, 31] set([0, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 75 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517288 none O=C([O-])C1=C2CCCCC2=C(C(=O)NC2=CC=C(N3CCCCC3)C=N2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 5, 5, 5, 5, 1, 1, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 11, 11, 11, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 8, 8, 35, 35, 35, 35, 35, 35, 35, 35, 35, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8] 35 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48]) total number of confs: 53 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517288 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517288 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517288/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517288 Building REAL300004517289 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517289' /scratch/stefan/7774842/working/building/REAL300004517289 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517289 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517289/0 /scratch/stefan/7774842/working/building/REAL300004517289 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 323) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/323 `/scratch/stefan/7774842/working/3D/323' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C12CCC(C(=O)NC3=CC=C(N4CCCCC4)C=N3)(CC1)CC2) `REAL300004517289.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517289.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517289/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517289 none O=C([O-])C12CCC(C(=O)NC3=CC=C(N4CCCCC4)C=N3)(CC1)CC2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [9, 3, 9, 3, 9, 9, 3, 3, 3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 3, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 9, 9, 9, 9, 9, 9, 9, 9] 24 rigid atoms, others: [32, 43, 9, 10, 11, 12, 13, 14, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 55 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517289 none O=C([O-])C12CCC(C(=O)NC3=CC=C(N4CCCCC4)C=N3)(CC1)CC2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 6, 6, 7, 9, 9, 9, 9, 24, 24, 24, 24, 24, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 7, 9, 9, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 9, 1, 1, 1, 1, 1, 1, 1, 1] 24 rigid atoms, others: [1, 3, 4, 5, 6, 7, 22, 23, 24, 25, 26, 27, 28, 29, 44, 45, 46, 47, 48, 49, 50, 51] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517289 none O=C([O-])C12CCC(C(=O)NC3=CC=C(N4CCCCC4)C=N3)(CC1)CC2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 1, 8, 5, 5, 5, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [24, 13, 24, 13, 24, 24, 13, 13, 13, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 24, 24, 24, 13, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 24, 24, 24, 24, 24, 24, 24, 24] 24 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 154 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517289 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517289 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517289/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517289 Building REAL300004517290 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517290' /scratch/stefan/7774842/working/building/REAL300004517290 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517290 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517290/0 /scratch/stefan/7774842/working/building/REAL300004517290 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 324) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/324 `/scratch/stefan/7774842/working/3D/324' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)C3=CC=CC(OCC(=O)[O-])=C3)C=C21) `REAL300004517290.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517290.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517290/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517290 none CN1CCC2=CC=C(NC(=O)C3=CC=CC(OCC(=O)[O-])=C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 30, 30, 30, 30, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 7, 31, 42, 42, 1, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 30, 5, 1, 1, 1, 31, 31, 1, 30] 188 rigid atoms, others: [34, 35, 36, 39, 9, 11, 12, 13, 14, 15, 16, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 40]) total number of confs: 171 number of broken/clashed sets: 35 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517290 none CN1CCC2=CC=C(NC(=O)C3=CC=CC(OCC(=O)[O-])=C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 30, 30, 30, 30, 30, 95, 188, 188, 188, 30, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 9, 30, 30, 30, 188, 188, 30, 1] 188 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 40, 32, 22, 23, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 591 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517290 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517290 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517290/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517290 Building REAL300004517291 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517291' /scratch/stefan/7774842/working/building/REAL300004517291 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517291 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517291/0 /scratch/stefan/7774842/working/building/REAL300004517291 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 325) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/325 `/scratch/stefan/7774842/working/3D/325' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)C3=CC=C(C(=O)[O-])S3)C=C21) `REAL300004517291.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517291/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517291 none CN1CCC2=CC=C(NC(=O)C3=CC=C(C(=O)[O-])S3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 10, 1, 1, 16] 16 rigid atoms, others: [32, 9, 11, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 29 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517291 none CN1CCC2=CC=C(NC(=O)C3=CC=C(C(=O)[O-])S3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 16, 16, 16, 16, 16, 16, 16, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 8, 16, 16, 1] 16 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 33, 19, 20, 24, 25, 26, 27, 28, 29] set([32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 30, 31]) total number of confs: 35 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517291 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517291 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517291/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517291 Building REAL300004517292 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517292' /scratch/stefan/7774842/working/building/REAL300004517292 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517292 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517292/0 /scratch/stefan/7774842/working/building/REAL300004517292 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 326) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/326 `/scratch/stefan/7774842/working/3D/326' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(SC1=CC=CC=C1C(=O)NC1=CC=C2CCN(C)C2=C1)C(=O)[O-]) `REAL300004517292.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517292.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517292/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517292 none CC(SC1=CC=CC=C1C(=O)NC1=CC=C2CCN(C)C2=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 11, 11, 11, 7, 11, 11, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 11, 11, 11, 11, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1] 17 rigid atoms, others: [34, 35, 36, 37, 38, 39, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42]) total number of confs: 53 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517292 none CC(SC1=CC=CC=C1C(=O)NC1=CC=C2CCN(C)C2=C1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 1, 1, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 7, 7, 6, 6, 6, 6, 1, 1, 1, 1, 4, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 17 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 9, 29, 30, 31] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517292 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517292 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517292/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517292 Building REAL300004517293 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517293' /scratch/stefan/7774842/working/building/REAL300004517293 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517293 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517293/0 /scratch/stefan/7774842/working/building/REAL300004517293 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 327) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/327 `/scratch/stefan/7774842/working/3D/327' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C(=O)NC2=CC=C3CCN(C)C3=C2)=CC=C1OCC(=O)[O-]) `REAL300004517293.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517293/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517293 none CCOC1=CC(C(=O)NC2=CC=C3CCN(C)C3=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [63, 50, 17, 17, 17, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 91, 194, 200, 200, 63, 63, 63, 63, 63, 17, 6, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 17, 17, 194, 194] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 44, 45, 46, 47]) total number of confs: 771 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517293 none CCOC1=CC(C(=O)NC2=CC=C3CCN(C)C3=C2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 8, 1, 1, 1, 1, 1, 5, 5, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 9, 32, 53, 53, 19, 19, 19, 19, 19, 1, 5, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 32, 32] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 44, 45, 19, 20, 21, 22] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517293 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517293 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517293/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517293 Building REAL300004517294 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517294' /scratch/stefan/7774842/working/building/REAL300004517294 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517294 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517294/0 /scratch/stefan/7774842/working/building/REAL300004517294 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 328) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/328 `/scratch/stefan/7774842/working/3D/328' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)CCC3=CC=C(C(=O)[O-])C=C3)C=C21) `REAL300004517294.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517294/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517294 none CN1CCC2=CC=C(NC(=O)CCC3=CC=C(C(=O)[O-])C=C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [48, 48, 48, 48, 48, 48, 48, 20, 19, 6, 19, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 20, 6, 6, 4, 4, 1, 1, 1, 1, 48] 48 rigid atoms, others: [38, 39, 40, 41, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42]) total number of confs: 104 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517294 none CN1CCC2=CC=C(NC(=O)CCC3=CC=C(C(=O)[O-])C=C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 29, 38, 48, 48, 38, 38, 48, 48, 48, 48, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 10, 29, 29, 38, 38, 48, 48, 48, 48, 1] 48 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 42, 32, 22, 23, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 244 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517294 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517294 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517294/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517294 Building REAL300004517295 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517295' /scratch/stefan/7774842/working/building/REAL300004517295 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517295 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517295/0 /scratch/stefan/7774842/working/building/REAL300004517295 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 329) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/329 `/scratch/stefan/7774842/working/3D/329' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)C=CC3=CC=C(C(=O)[O-])C=C3)C=C21) `REAL300004517295.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517295 none CN1CCC2=CC=C(NC(=O)C=CC3=CC=C(C(=O)[O-])C=C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 24, 24, 24, 13, 13, 3, 13, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 13, 3, 3, 1, 1, 1, 1, 24] 24 rigid atoms, others: [36, 37, 38, 39, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40]) total number of confs: 49 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517295 none CN1CCC2=CC=C(NC(=O)C=CC3=CC=C(C(=O)[O-])C=C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 22, 23, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 9, 24, 24, 24, 24, 24, 24, 1] 24 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 40, 32, 22, 23, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 75 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517295 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517295 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517295/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517295 Building REAL300004517296 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517296' /scratch/stefan/7774842/working/building/REAL300004517296 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517296 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517296/0 /scratch/stefan/7774842/working/building/REAL300004517296 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 330) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/330 `/scratch/stefan/7774842/working/3D/330' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)CNS(=O)(=O)C3=CC=C(C(=O)[O-])C=C3)C=C21) `REAL300004517296.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517296.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517296/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517296 none CN1CCC2=CC=C(NC(=O)CNS(=O)(=O)C3=CC=C(C(=O)[O-])C=C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 98, 98, 27, 98, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 98, 27, 27, 5, 1, 1, 1, 1, 201] 201 rigid atoms, others: [40, 41, 42, 43, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44]) total number of confs: 450 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517296 none CN1CCC2=CC=C(NC(=O)CNS(=O)(=O)C3=CC=C(C(=O)[O-])C=C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 66, 139, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 9, 66, 66, 139, 201, 201, 201, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 7, 44, 34, 35, 25, 26, 5, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 798 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517296 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517296 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517296/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517296 Building REAL300004517297 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517297' /scratch/stefan/7774842/working/building/REAL300004517297 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517297 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517297/0 /scratch/stefan/7774842/working/building/REAL300004517297 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 331) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/331 `/scratch/stefan/7774842/working/3D/331' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)C3=CC(C(=O)[O-])=CC([N+](=O)[O-])=C3)C=C21) `REAL300004517297.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517297/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517297 none CN1CCC2=CC=C(NC(=O)C3=CC(C(=O)[O-])=CC([N+](=O)[O-])=C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 5, 5, 1, 5, 1, 1, 1, 1, 2, 2, 1, 1, 1, 2, 2, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 1, 1, 1, 13] 13 rigid atoms, others: [35, 36, 37, 9, 11, 12, 13, 14, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 15, 16, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38]) total number of confs: 31 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517297 none CN1CCC2=CC=C(NC(=O)C3=CC(C(=O)[O-])=CC([N+](=O)[O-])=C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 5, 13, 13, 13, 1] 13 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 7, 23, 24, 33, 38, 28, 29, 30, 31] set([34, 35, 36, 37, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27]) total number of confs: 29 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517297 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517297 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517297/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517297 Building REAL300004517298 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517298' /scratch/stefan/7774842/working/building/REAL300004517298 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517298 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517298/0 /scratch/stefan/7774842/working/building/REAL300004517298 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 332) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/332 `/scratch/stefan/7774842/working/3D/332' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)C3=CC(C(=O)[O-])=CC([N+](=O)[O-])=C3)C=C21) `REAL300004517298.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517298 none CN1CCC2=CC=C(NC(=O)C3=CC(C(=O)[O-])=CC([N+](=O)[O-])=C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 5, 5, 1, 5, 1, 1, 1, 1, 2, 2, 1, 1, 1, 2, 2, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 1, 1, 1, 13] 13 rigid atoms, others: [35, 36, 37, 9, 11, 12, 13, 14, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 15, 16, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38]) total number of confs: 31 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517298 none CN1CCC2=CC=C(NC(=O)C3=CC(C(=O)[O-])=CC([N+](=O)[O-])=C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 5, 13, 13, 13, 1] 13 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 7, 23, 24, 33, 38, 28, 29, 30, 31] set([34, 35, 36, 37, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27]) total number of confs: 29 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517298 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517298 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517298/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517298 Building REAL300004517299 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517299' /scratch/stefan/7774842/working/building/REAL300004517299 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517299 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517299/0 /scratch/stefan/7774842/working/building/REAL300004517299 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 333) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/333 `/scratch/stefan/7774842/working/3D/333' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=NN1C1=CC=C(C(=O)NC2=CC=C3CCN(C)C3=C2)C=C1) `REAL300004517299.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517299.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517299/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517299 none CC1=C(C(=O)[O-])C=NN1C1=CC=C(C(=O)NC2=CC=C3CCN(C)C3=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 8, 8, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 9, 9, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 5, 5, 5, 5, 1, 1, 7, 32, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1] 52 rigid atoms, others: [32, 33, 8, 9, 10, 11, 12, 13, 46, 45, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 67 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517299 none CC1=C(C(=O)[O-])C=NN1C1=CC=C(C(=O)NC2=CC=C3CCN(C)C3=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 8, 8, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 5, 5, 1, 1, 19, 19, 19, 52, 52, 52, 52, 52, 52, 52, 52, 52, 5, 5, 2, 2, 2, 1, 5, 5, 19, 52, 52, 52, 52, 52, 52, 52, 52, 52, 52, 5, 5] 52 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 9, 31] set([4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 110 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517299 none CC1=C(C(=O)[O-])C=NN1C1=CC=C(C(=O)NC2=CC=C3CCN(C)C3=C2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 8, 8, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 52, 52, 52, 52, 52, 52, 32, 32, 32, 32, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 52, 52, 52, 52, 32, 32, 9, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 32, 32] 52 rigid atoms, others: [35, 36, 37, 38, 39, 40, 44, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27, 28, 29, 30, 31, 32, 33, 34, 41, 42, 43, 45, 46]) total number of confs: 96 number of broken/clashed sets: 10 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517299 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517299 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517299/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517299 Building REAL300004517300 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517300' /scratch/stefan/7774842/working/building/REAL300004517300 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517300 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517300/0 /scratch/stefan/7774842/working/building/REAL300004517300 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 334) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/334 `/scratch/stefan/7774842/working/3D/334' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)C3=CC(C(=O)[O-])=NN3C3=CC=CC=C3)C=C21) `REAL300004517300.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517300.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517300/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517300 none CN1CCC2=CC=C(NC(=O)C3=CC(C(=O)[O-])=NN3C3=CC=CC=C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 11, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 43, 43, 43, 12, 12, 1, 12, 1, 1, 1, 1, 2, 2, 1, 1, 1, 6, 6, 1, 6, 6, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 12, 1, 6, 6, 1, 6, 6, 43] 47 rigid atoms, others: [37, 9, 11, 12, 13, 14, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42, 43]) total number of confs: 82 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517300 none CN1CCC2=CC=C(NC(=O)C3=CC(C(=O)[O-])=NN3C3=CC=CC=C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 11, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 43, 43, 43, 43, 43, 43, 43, 43, 47, 47, 43, 47, 47, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 9, 43, 47, 47, 43, 47, 47, 1] 47 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 7, 34, 43, 35, 25, 26, 5, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 87 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517300 none CN1CCC2=CC=C(NC(=O)C3=CC(C(=O)[O-])=NN3C3=CC=CC=C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 11, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 47, 47, 47, 22, 22, 6, 22, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 22, 6, 1, 1, 1, 1, 1, 47] 47 rigid atoms, others: [38, 39, 40, 41, 42, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43]) total number of confs: 87 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517300 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517300 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517300/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517300 Building REAL300004517301 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517301' /scratch/stefan/7774842/working/building/REAL300004517301 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517301 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517301/0 /scratch/stefan/7774842/working/building/REAL300004517301 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 335) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/335 `/scratch/stefan/7774842/working/3D/335' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)CCC3=CC=CC=C3C(=O)[O-])C=C21) `REAL300004517301.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517301.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517301/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517301 none CN1CCC2=CC=C(NC(=O)CCC3=CC=CC=C3C(=O)[O-])C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 59, 59, 59, 59, 24, 24, 9, 24, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 59, 59, 59, 59, 59, 59, 59, 59, 59, 59, 59, 24, 9, 9, 5, 5, 1, 1, 1, 1, 59] 59 rigid atoms, others: [38, 39, 40, 41, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42]) total number of confs: 138 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517301 none CN1CCC2=CC=C(NC(=O)CCC3=CC=CC=C3C(=O)[O-])C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 40, 54, 59, 59, 59, 59, 59, 59, 59, 59, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 9, 40, 40, 54, 54, 59, 59, 59, 59, 1] 59 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 42, 32, 22, 23, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517301 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517301 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517301/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517301 Building REAL300004517302 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517302' /scratch/stefan/7774842/working/building/REAL300004517302 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517302 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517302/0 /scratch/stefan/7774842/working/building/REAL300004517302 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 336) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/336 `/scratch/stefan/7774842/working/3D/336' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)NC2=CC=C3CCN(C)C3=C2)=CC(C)=C1OCC(=O)[O-]) `REAL300004517302.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517302 none CC1=CC(C(=O)NC2=CC=C3CCN(C)C3=C2)=CC(C)=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 1, 1, 5, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [37, 37, 37, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 15, 37, 58, 100, 100, 100, 37, 37, 37, 37, 9, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 37, 37, 37, 37, 100, 100] 100 rigid atoms, others: [32, 33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 40, 31] set([0, 1, 2, 3, 4, 5, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 41, 42, 43, 44, 45, 46]) total number of confs: 390 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517302 none CC1=CC(C(=O)NC2=CC=C3CCN(C)C3=C2)=CC(C)=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 1, 1, 5, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 7, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 1, 1, 1, 1, 2, 14, 22, 22, 2, 2, 2, 1, 7, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 1, 2, 2, 2, 14, 14] 100 rigid atoms, others: [0, 1, 2, 3, 4, 41, 17, 18, 19, 20, 21, 29] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517302 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517302 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517302/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517302 Building REAL300004517303 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517303' /scratch/stefan/7774842/working/building/REAL300004517303 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517303 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517303/0 /scratch/stefan/7774842/working/building/REAL300004517303 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 337) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/337 `/scratch/stefan/7774842/working/3D/337' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)CC3=CC=CC(C(=O)[O-])=C3)C=C21) `REAL300004517303.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517303.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517303/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517303 none CN1CCC2=CC=C(NC(=O)CC3=CC=CC(C(=O)[O-])=C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 58, 58, 58, 57, 17, 17, 7, 17, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 17, 7, 7, 1, 1, 1, 1, 58] 58 rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 14, 15, 16, 17, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39]) total number of confs: 117 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517303 none CN1CCC2=CC=C(NC(=O)CC3=CC=CC(C(=O)[O-])=C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 23, 58, 58, 58, 58, 58, 58, 58, 58, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 10, 23, 23, 58, 58, 58, 58, 1] 58 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 39, 21, 22, 26, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 129 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517303 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517303 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517303/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517303 Building REAL300004517304 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517304' /scratch/stefan/7774842/working/building/REAL300004517304 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517304 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517304/0 /scratch/stefan/7774842/working/building/REAL300004517304 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 338) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/338 `/scratch/stefan/7774842/working/3D/338' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)C3CCCC(C(=O)[O-])C3)C=C21) `REAL300004517304.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517304.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517304/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517304 none CN1CCC2=CC=C(NC(=O)C3CCCC(C(=O)[O-])C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [43, 43, 43, 43, 43, 43, 43, 13, 12, 1, 12, 1, 1, 1, 1, 1, 1, 3, 3, 1, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43] 43 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 9, 11, 12, 13, 14, 15, 16, 19, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 42]) total number of confs: 74 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517304 none CN1CCC2=CC=C(NC(=O)C3CCCC(C(=O)[O-])C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 10, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 1] 43 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 42, 20, 21, 25, 26, 27, 28, 29, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517304 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517304 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517304/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517304 Building REAL300004517305 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517305' /scratch/stefan/7774842/working/building/REAL300004517305 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517305 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517305/0 /scratch/stefan/7774842/working/building/REAL300004517305 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 339) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/339 `/scratch/stefan/7774842/working/3D/339' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)C3=CC=C(C(=O)[O-])C=C3F)C=C21) `REAL300004517305.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517305 none CN1CCC2=CC=C(NC(=O)C3=CC=C(C(=O)[O-])C=C3F)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 12, 1, 1, 1, 21] 21 rigid atoms, others: [33, 34, 35, 9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36]) total number of confs: 39 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517305 none CN1CCC2=CC=C(NC(=O)C3=CC=C(C(=O)[O-])C=C3F)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 9, 21, 21, 21, 1] 21 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 36, 26, 27, 28, 29, 30, 31] set([32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517305 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517305 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517305/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517305 Building REAL300004517306 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517306' /scratch/stefan/7774842/working/building/REAL300004517306 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517306 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517306/0 /scratch/stefan/7774842/working/building/REAL300004517306 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 340) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/340 `/scratch/stefan/7774842/working/3D/340' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)[C@H]3CC[C@H](C(=O)[O-])CC3)C=C21) `REAL300004517306.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517306/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517306 none CN1CCC2=CC=C(NC(=O)[C@H]3CC[C@H](C(=O)[O-])CC3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 11, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 33, 33, 8, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 8, 1, 1, 1, 1, 1, 1, 1, 1, 33] 33 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 9, 11, 12, 13, 14, 15, 16, 17, 20, 21, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 42]) total number of confs: 56 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517306 none CN1CCC2=CC=C(NC(=O)[C@H]3CC[C@H](C(=O)[O-])CC3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 11, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 8, 33, 33, 33, 33, 33, 33, 33, 33, 1] 33 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 42, 32, 22, 23, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517306 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517306 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517306/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517306 Building REAL300004517307 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517307' /scratch/stefan/7774842/working/building/REAL300004517307 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517307 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517307/0 /scratch/stefan/7774842/working/building/REAL300004517307 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 341) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/341 `/scratch/stefan/7774842/working/3D/341' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)C3CCC(C(=O)[O-])CC3)C=C21) `REAL300004517307.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517307/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517307 none CN1CCC2=CC=C(NC(=O)C3CCC(C(=O)[O-])CC3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 1, 11, 11, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 35, 7, 6, 1, 6, 1, 1, 1, 1, 1, 3, 3, 1, 1, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35] 35 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 9, 11, 12, 13, 14, 15, 18, 19, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 42]) total number of confs: 57 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517307 none CN1CCC2=CC=C(NC(=O)C3CCC(C(=O)[O-])CC3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 1, 11, 11, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 7, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1] 35 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 42, 20, 21, 25, 26, 27, 28, 29, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517307 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517307 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517307/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517307 Building REAL300004517308 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517308' /scratch/stefan/7774842/working/building/REAL300004517308 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517308 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517308/0 /scratch/stefan/7774842/working/building/REAL300004517308 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 342) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/342 `/scratch/stefan/7774842/working/3D/342' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)CC3=CC=C(C(=O)[O-])C=C3)C=C21) `REAL300004517308.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517308/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517308 none CN1CCC2=CC=C(NC(=O)CC3=CC=C(C(=O)[O-])C=C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 37, 37, 37, 37, 37, 9, 9, 4, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 9, 4, 4, 1, 1, 1, 1, 37] 37 rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 14, 15, 16, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39]) total number of confs: 69 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517308 none CN1CCC2=CC=C(NC(=O)CC3=CC=C(C(=O)[O-])C=C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 25, 37, 37, 31, 37, 37, 37, 37, 37, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 11, 25, 25, 37, 37, 37, 37, 1] 37 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 39, 21, 22, 26, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517308 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517308 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517308/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517308 Building REAL300004517309 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517309' /scratch/stefan/7774842/working/building/REAL300004517309 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517309 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517309/0 /scratch/stefan/7774842/working/building/REAL300004517309 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 343) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/343 `/scratch/stefan/7774842/working/3D/343' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)CN3C=C(C(=O)[O-])N=N3)C=C21) `REAL300004517309.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517309 none CN1CCC2=CC=C(NC(=O)CN3C=C(C(=O)[O-])N=N3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 8, 1, 1, 1, 11, 11, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [116, 116, 116, 116, 116, 116, 116, 47, 47, 8, 47, 1, 1, 1, 1, 1, 2, 2, 1, 1, 116, 116, 116, 116, 116, 116, 116, 116, 116, 116, 116, 47, 8, 8, 1, 116] 116 rigid atoms, others: [34, 11, 12, 13, 14, 15, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35]) total number of confs: 226 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517309 none CN1CCC2=CC=C(NC(=O)CN3C=C(C(=O)[O-])N=N3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 8, 1, 1, 1, 11, 11, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 116 conformations in input total number of sets (complete confs): 116 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 58, 116, 116, 116, 116, 116, 116, 116, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 11, 58, 58, 116, 1] 116 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 35, 20, 21, 25, 26, 27, 28, 29, 30] set([32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 31]) total number of confs: 289 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517309 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517309 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517309/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517309 Building REAL300004517310 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517310' /scratch/stefan/7774842/working/building/REAL300004517310 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517310 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517310/0 /scratch/stefan/7774842/working/building/REAL300004517310 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 344) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/344 `/scratch/stefan/7774842/working/3D/344' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C(=O)NC2=CC=C3CCN(C)C3=C2)=CC=C1C(=O)[O-]) `REAL300004517310.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517310.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517310/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517310 none CC1=NC(C(=O)NC2=CC=C3CCN(C)C3=C2)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 9, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 13, 13] 13 rigid atoms, others: [32, 36, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 35, 33, 34, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 38, 37]) total number of confs: 33 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517310 none CC1=NC(C(=O)NC2=CC=C3CCN(C)C3=C2)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 5, 5, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 3, 3, 2, 2, 2, 6, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1] 13 rigid atoms, others: [0, 1, 2, 3, 4, 37, 38, 17, 18, 19, 20] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517310 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517310 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517310/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517310 Building REAL300004517311 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517311' /scratch/stefan/7774842/working/building/REAL300004517311 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517311 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517311/0 /scratch/stefan/7774842/working/building/REAL300004517311 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 345) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/345 `/scratch/stefan/7774842/working/3D/345' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)C3=CC(Br)=CC(C(=O)[O-])=C3)C=C21) `REAL300004517311.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517311.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517311/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517311 none CN1CCC2=CC=C(NC(=O)C3=CC(Br)=CC(C(=O)[O-])=C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 17, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 1, 1, 1, 13] 13 rigid atoms, others: [33, 34, 35, 9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36]) total number of confs: 23 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517311 none CN1CCC2=CC=C(NC(=O)C3=CC(Br)=CC(C(=O)[O-])=C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 17, 1, 1, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 5, 13, 13, 13, 1] 13 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 36, 26, 27, 28, 29, 30, 31] set([32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25]) total number of confs: 29 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517311 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517311 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517311/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517311 Building REAL300004517312 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517312' /scratch/stefan/7774842/working/building/REAL300004517312 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517312 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517312/0 /scratch/stefan/7774842/working/building/REAL300004517312 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 346) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/346 `/scratch/stefan/7774842/working/3D/346' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)C3=CC=CC(CC(=O)[O-])=C3)C=C21) `REAL300004517312.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517312/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517312 none CN1CCC2=CC=C(NC(=O)C3=CC=CC(CC(=O)[O-])=C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 2, 3, 3, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 5, 1, 1, 1, 2, 2, 1, 17] 25 rigid atoms, others: [33, 34, 35, 38, 9, 11, 12, 13, 14, 15, 16, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 39]) total number of confs: 37 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517312 none CN1CCC2=CC=C(NC(=O)C3=CC=CC(CC(=O)[O-])=C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 17, 17, 17, 17, 17, 25, 25, 25, 17, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 5, 17, 17, 17, 25, 25, 17, 1] 25 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 39, 21, 22, 26, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 81 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517312 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517312 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517312/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517312 Building REAL300004517313 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517313' /scratch/stefan/7774842/working/building/REAL300004517313 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517313 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517313/0 /scratch/stefan/7774842/working/building/REAL300004517313 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 347) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/347 `/scratch/stefan/7774842/working/3D/347' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)C3=CC=CC=C3C3=CC=CC=C3C(=O)[O-])C=C21) `REAL300004517313.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517313.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517313/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517313 none CN1CCC2=CC=C(NC(=O)C3=CC=CC=C3C3=CC=CC=C3C(=O)[O-])C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 5, 1, 1, 1, 1, 5, 5, 5, 5, 26] 31 rigid atoms, others: [38, 39, 40, 9, 11, 12, 13, 14, 15, 16, 17, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46]) total number of confs: 49 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517313 none CN1CCC2=CC=C(NC(=O)C3=CC=CC=C3C3=CC=CC=C3C(=O)[O-])C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 26, 26, 26, 26, 26, 26, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 9, 26, 26, 26, 26, 31, 31, 31, 31, 1] 31 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 7, 34, 46, 35, 36, 26, 27, 5, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517313 none CN1CCC2=CC=C(NC(=O)C3=CC=CC=C3C3=CC=CC=C3C(=O)[O-])C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 31, 31, 7, 7, 5, 7, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 7, 5, 5, 5, 5, 1, 1, 1, 1, 31] 31 rigid atoms, others: [42, 43, 44, 45, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46]) total number of confs: 50 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517313 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517313 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517313/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517313 Building REAL300004517314 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517314' /scratch/stefan/7774842/working/building/REAL300004517314 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517314 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517314/0 /scratch/stefan/7774842/working/building/REAL300004517314 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 348) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/348 `/scratch/stefan/7774842/working/3D/348' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)C3=C(CC(=O)[O-])OC=C3)C=C21) `REAL300004517314.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517314/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517314 none CN1CCC2=CC=C(NC(=O)C3=C(CC(=O)[O-])OC=C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 5, 1, 11, 11, 12, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 14, 5, 5, 1, 5, 1, 1, 1, 2, 6, 6, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 5, 2, 2, 1, 1, 14] 14 rigid atoms, others: [34, 35, 9, 11, 12, 13, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 42 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517314 none CN1CCC2=CC=C(NC(=O)C3=C(CC(=O)[O-])OC=C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 5, 1, 11, 11, 12, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 8, 14, 14, 14, 14, 1] 14 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 25, 26, 27, 28, 29, 30, 36] set([32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 31]) total number of confs: 33 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517314 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517314 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517314/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517314 Building REAL300004517315 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517315' /scratch/stefan/7774842/working/building/REAL300004517315 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517315 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517315/0 /scratch/stefan/7774842/working/building/REAL300004517315 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 349) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/349 `/scratch/stefan/7774842/working/3D/349' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=COC(CC(=O)[O-])=C1C(=O)NC1=CC=C2CCN(C)C2=C1) `REAL300004517315.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517315/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517315 none CC1=COC(CC(=O)[O-])=C1C(=O)NC1=CC=C2CCN(C)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 5, 1, 11, 11, 1, 1, 11, 8, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 8, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1] 14 rigid atoms, others: [32, 33, 34, 35, 39, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 36, 37, 38]) total number of confs: 33 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517315 none CC1=COC(CC(=O)[O-])=C1C(=O)NC1=CC=C2CCN(C)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 5, 1, 11, 11, 1, 1, 11, 8, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 6, 6, 1, 1, 5, 5, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 1, 2, 2, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 14 rigid atoms, others: [0, 1, 2, 3, 4, 5, 9, 10, 26] set([6, 7, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517315 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517315 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517315/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517315 Building REAL300004517316 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517316' /scratch/stefan/7774842/working/building/REAL300004517316 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517316 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517316/0 /scratch/stefan/7774842/working/building/REAL300004517316 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 350) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/350 `/scratch/stefan/7774842/working/3D/350' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)CC3CCC(C(=O)[O-])CC3)C=C21) `REAL300004517316.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517316/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517316 none CN1CCC2=CC=C(NC(=O)CC3CCC(C(=O)[O-])CC3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [73, 73, 73, 73, 73, 73, 73, 32, 32, 10, 32, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 73, 73, 73, 73, 73, 73, 73, 73, 73, 73, 73, 32, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 73] 73 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 43, 19, 20, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 45]) total number of confs: 150 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517316 none CN1CCC2=CC=C(NC(=O)CC3CCC(C(=O)[O-])CC3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 73 conformations in input total number of sets (complete confs): 73 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 57, 72, 73, 73, 73, 73, 73, 73, 73, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 11, 57, 57, 73, 73, 73, 73, 73, 73, 73, 73, 73, 73, 1] 73 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 45, 21, 22, 26, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 250 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517316 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517316 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517316/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517316 Building REAL300004517317 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517317' /scratch/stefan/7774842/working/building/REAL300004517317 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517317 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517317/0 /scratch/stefan/7774842/working/building/REAL300004517317 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 351) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/351 `/scratch/stefan/7774842/working/3D/351' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)C34CCC(C(=O)[O-])(CC3)C4)C=C21) `REAL300004517317.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517317 none CN1CCC2=CC=C(NC(=O)C34CCC(C(=O)[O-])(CC3)C4)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 34, 34, 34, 7, 7, 1, 7, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34] 34 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 18, 19, 20, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 43]) total number of confs: 54 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517317 none CN1CCC2=CC=C(NC(=O)C34CCC(C(=O)[O-])(CC3)C4)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 11, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1] 34 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 43, 21, 22, 26, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517317 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517317 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517317/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517317 Building REAL300004517318 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517318' /scratch/stefan/7774842/working/building/REAL300004517318 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517318 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517318/0 /scratch/stefan/7774842/working/building/REAL300004517318 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 352) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/352 `/scratch/stefan/7774842/working/3D/352' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)C34CCC(C(=O)[O-])(CC3)CC4)C=C21) `REAL300004517318.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517318 none CN1CCC2=CC=C(NC(=O)C34CCC(C(=O)[O-])(CC3)CC4)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11] 11 rigid atoms, others: [9, 11, 12, 13, 14, 15, 18, 19, 20, 21, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 46]) total number of confs: 25 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517318 none CN1CCC2=CC=C(NC(=O)C34CCC(C(=O)[O-])(CC3)CC4)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 11, 11, 7, 7, 11, 11, 11, 11, 11, 11, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1] 11 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 46, 32, 22, 23, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517318 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517318 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517318/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517318 Building REAL300004517319 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517319' /scratch/stefan/7774842/working/building/REAL300004517319 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517319 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517319/0 /scratch/stefan/7774842/working/building/REAL300004517319 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 353) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/353 `/scratch/stefan/7774842/working/3D/353' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)C3=CC=NC4=C(C(=O)[O-])C=NN43)C=C21) `REAL300004517319.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517319.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517319/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517319 none CN1CCC2=CC=C(NC(=O)C3=CC=NC4=C(C(=O)[O-])C=NN43)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 15, 15, 6, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 6, 1, 1, 1, 15] 15 rigid atoms, others: [35, 36, 37, 9, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38]) total number of confs: 33 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517319 none CN1CCC2=CC=C(NC(=O)C3=CC=NC4=C(C(=O)[O-])C=NN43)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 9, 15, 15, 15, 1] 15 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 7, 23, 24, 33, 38, 28, 29, 30, 31] set([34, 35, 36, 37, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27]) total number of confs: 36 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517319 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517319 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517319/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517319 Building REAL300004517320 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517320' /scratch/stefan/7774842/working/building/REAL300004517320 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517320 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517320/0 /scratch/stefan/7774842/working/building/REAL300004517320 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 354) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/354 `/scratch/stefan/7774842/working/3D/354' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)C3=C(CC(=O)[O-])C4=CC=CC=C4N3)C=C21) `REAL300004517320.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517320.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517320/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517320 none CN1CCC2=CC=C(NC(=O)C3=C(CC(=O)[O-])C4=CC=CC=C4N3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 15, 15, 5, 5, 1, 5, 1, 1, 1, 2, 7, 7, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 2, 2, 1, 1, 1, 1, 1, 15] 15 rigid atoms, others: [38, 39, 40, 9, 41, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43]) total number of confs: 45 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517320 none CN1CCC2=CC=C(NC(=O)C3=C(CC(=O)[O-])C4=CC=CC=C4N3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 1] 15 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 7, 34, 43, 24, 25, 33, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 33 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517320 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517320 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517320/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517320 Building REAL300004517321 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517321' /scratch/stefan/7774842/working/building/REAL300004517321 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517321 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517321/0 /scratch/stefan/7774842/working/building/REAL300004517321 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 355) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/355 `/scratch/stefan/7774842/working/3D/355' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)CC3CCCC4=CC=C(C(=O)[O-])C=C43)C=C21) `REAL300004517321.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517321.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517321/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517321 none CN1CCC2=CC=C(NC(=O)CC3CCCC4=CC=C(C(=O)[O-])C=C43)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 47, 47, 47, 18, 18, 7, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 18, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47] 47 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 49]) total number of confs: 94 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517321 none CN1CCC2=CC=C(NC(=O)CC3CCCC4=CC=C(C(=O)[O-])C=C43)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 36, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 11, 36, 36, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1] 47 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 7, 34, 49, 35, 25, 26, 5, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 172 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517321 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517321 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517321/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517321 Building REAL300004517322 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517322' /scratch/stefan/7774842/working/building/REAL300004517322 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517322 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517322/0 /scratch/stefan/7774842/working/building/REAL300004517322 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 356) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/356 `/scratch/stefan/7774842/working/3D/356' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2=CC=C3CCN(C)C3=C2)C=C(C(=O)[O-])O1) `REAL300004517322.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517322.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517322/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517322 none CC1=C(C(=O)NC2=CC=C3CCN(C)C3=C2)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 8, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 18] 18 rigid atoms, others: [35, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 33, 32, 34, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 36]) total number of confs: 39 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517322 none CC1=C(C(=O)NC2=CC=C3CCN(C)C3=C2)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 7, 7, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1] 18 rigid atoms, others: [0, 1, 2, 3, 36, 16, 17, 18, 19, 20, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 38 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517322 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517322 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517322/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517322 Building REAL300004517323 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517323' /scratch/stefan/7774842/working/building/REAL300004517323 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517323 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517323/0 /scratch/stefan/7774842/working/building/REAL300004517323 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 357) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/357 `/scratch/stefan/7774842/working/3D/357' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])OC(C(=O)NC2=CC=C3CCN(C)C3=C2)=C1) `REAL300004517323.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517323.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517323/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517323 none CC1=C(C(=O)[O-])OC(C(=O)NC2=CC=C3CCN(C)C3=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 1, 11, 8, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 9, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 18] 18 rigid atoms, others: [35, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 34, 21, 22, 23, 24, 25, 33, 36]) total number of confs: 38 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517323 none CC1=C(C(=O)[O-])OC(C(=O)NC2=CC=C3CCN(C)C3=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 1, 11, 8, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 6, 6, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 2, 2, 2, 6, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1] 18 rigid atoms, others: [0, 1, 2, 3, 36, 6, 7, 8, 21] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 39 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517323 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517323 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517323/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517323 Building REAL300004517324 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517324' /scratch/stefan/7774842/working/building/REAL300004517324 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517324 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517324/0 /scratch/stefan/7774842/working/building/REAL300004517324 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 358) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/358 `/scratch/stefan/7774842/working/3D/358' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)CN3C=C(C(=O)[O-])C=N3)C=C21) `REAL300004517324.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517324.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517324/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517324 none CN1CCC2=CC=C(NC(=O)CN3C=C(C(=O)[O-])C=N3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 8, 1, 1, 1, 11, 11, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [118, 118, 118, 118, 118, 118, 118, 46, 46, 8, 46, 1, 1, 1, 1, 1, 1, 1, 1, 1, 118, 118, 118, 118, 118, 118, 118, 118, 118, 118, 118, 46, 8, 8, 1, 1, 118] 118 rigid atoms, others: [34, 35, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 224 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517324 none CN1CCC2=CC=C(NC(=O)CN3C=C(C(=O)[O-])C=N3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 8, 1, 1, 1, 11, 11, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 118 conformations in input total number of sets (complete confs): 118 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 50, 118, 118, 118, 118, 118, 118, 118, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 118, 118, 1] 118 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 25, 26, 27, 28, 29, 30, 36] set([32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 31]) total number of confs: 274 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517324 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517324 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517324/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517324 Building REAL300004517325 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517325' /scratch/stefan/7774842/working/building/REAL300004517325 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517325 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517325/0 /scratch/stefan/7774842/working/building/REAL300004517325 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 359) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/359 `/scratch/stefan/7774842/working/3D/359' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)C3=CC=C(C=CC(=O)[O-])O3)C=C21) `REAL300004517325.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517325 none CN1CCC2=CC=C(NC(=O)C3=CC=C(C=CC(=O)[O-])O3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 6, 6, 1, 6, 1, 1, 1, 1, 1, 11, 11, 21, 21, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 6, 1, 1, 11, 11, 20] 41 rigid atoms, others: [33, 34, 9, 11, 12, 13, 14, 15, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37]) total number of confs: 89 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517325 none CN1CCC2=CC=C(NC(=O)C3=CC=C(C=CC(=O)[O-])O3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 20, 20, 20, 20, 41, 41, 41, 41, 20, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 9, 20, 20, 41, 41, 1] 41 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 37, 21, 22, 26, 27, 28, 29, 30, 31] set([32, 33, 34, 35, 36, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517325 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517325 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517325/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517325 Building REAL300004517326 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517326' /scratch/stefan/7774842/working/building/REAL300004517326 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517326 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517326/0 /scratch/stefan/7774842/working/building/REAL300004517326 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 360) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/360 `/scratch/stefan/7774842/working/3D/360' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)C3(C(=O)[O-])CC4(CCC4)C3)C=C21) `REAL300004517326.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517326.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517326/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517326 none CN1CCC2=CC=C(NC(=O)C3(C(=O)[O-])CC4(CCC4)C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 1, 11, 11, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 5, 5, 1, 5, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21] 21 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 9, 42, 11, 12, 15, 16, 17, 18, 19, 20, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 43]) total number of confs: 37 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517326 none CN1CCC2=CC=C(NC(=O)C3(C(=O)[O-])CC4(CCC4)C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 1, 11, 11, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 9, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1] 21 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 43, 21, 22, 26, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517326 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517326 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517326/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517326 Building REAL300004517327 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517327' /scratch/stefan/7774842/working/building/REAL300004517327 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517327 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517327/0 /scratch/stefan/7774842/working/building/REAL300004517327 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 361) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/361 `/scratch/stefan/7774842/working/3D/361' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)C3=CC=C(OCC(=O)[O-])C=C3)C=C21) `REAL300004517327.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517327.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517327/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517327 none CN1CCC2=CC=C(NC(=O)C3=CC=C(OCC(=O)[O-])C=C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 147 conformations in input total number of sets (complete confs): 147 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 4, 4, 1, 4, 1, 1, 1, 1, 1, 7, 34, 48, 48, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 4, 1, 1, 34, 34, 1, 1, 22] 147 rigid atoms, others: [34, 35, 38, 39, 9, 11, 12, 13, 14, 15, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 40]) total number of confs: 182 number of broken/clashed sets: 51 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517327 none CN1CCC2=CC=C(NC(=O)C3=CC=C(OCC(=O)[O-])C=C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 22, 22, 9, 21, 69, 146, 146, 146, 22, 22, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 9, 22, 22, 146, 146, 22, 22, 1] 146 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 40, 32, 22, 23, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 514 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517327 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517327 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517327/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517327 Building REAL300004517328 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517328' /scratch/stefan/7774842/working/building/REAL300004517328 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517328 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517328/0 /scratch/stefan/7774842/working/building/REAL300004517328 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 362) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/362 `/scratch/stefan/7774842/working/3D/362' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)C3CC(C(=O)[O-])=NN3C3=CC=CC=C3)C=C21) `REAL300004517328.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517328.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517328/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517328 none CN1CCC2=CC=C(NC(=O)C3CC(C(=O)[O-])=NN3C3=CC=CC=C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 5, 1, 1, 11, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 4, 4, 1, 4, 1, 1, 1, 1, 7, 7, 1, 1, 1, 4, 4, 1, 4, 4, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 4, 1, 1, 1, 4, 4, 1, 4, 4, 22] 26 rigid atoms, others: [37, 38, 39, 9, 11, 12, 13, 14, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44, 45]) total number of confs: 53 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517328 none CN1CCC2=CC=C(NC(=O)C3CC(C(=O)[O-])=NN3C3=CC=CC=C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 5, 1, 1, 11, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 22, 22, 22, 26, 26, 22, 22, 22, 26, 26, 22, 26, 26, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 10, 22, 22, 22, 26, 26, 26, 26, 26, 1] 26 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 7, 34, 45, 35, 25, 26, 5, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517328 none CN1CCC2=CC=C(NC(=O)C3CC(C(=O)[O-])=NN3C3=CC=CC=C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 5, 1, 1, 11, 11, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 26, 26, 26, 9, 9, 4, 9, 4, 4, 4, 4, 14, 14, 4, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 9, 4, 4, 4, 1, 1, 1, 1, 1, 26] 26 rigid atoms, others: [40, 41, 42, 43, 44, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 45]) total number of confs: 72 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517328 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517328 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517328/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517328 Building REAL300004517329 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517329' /scratch/stefan/7774842/working/building/REAL300004517329 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517329 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517329/0 /scratch/stefan/7774842/working/building/REAL300004517329 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 363) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/363 `/scratch/stefan/7774842/working/3D/363' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)C3=CC(C(=O)[O-])=NN3C)C=C21) `REAL300004517329.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517329/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517329 none CN1CCC2=CC=C(NC(=O)C3=CC(C(=O)[O-])=NN3C)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 11, 11, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 10, 10, 1, 10, 1, 1, 1, 1, 2, 2, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 10, 1, 2, 2, 2, 13] 13 rigid atoms, others: [32, 9, 11, 12, 13, 14, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36]) total number of confs: 35 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517329 none CN1CCC2=CC=C(NC(=O)C3=CC(C(=O)[O-])=NN3C)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 11, 11, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 7, 13, 13, 13, 13, 1] 13 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 25, 26, 27, 28, 29, 30, 36] set([32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 31]) total number of confs: 31 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517329 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517329 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517329/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517329 Building REAL300004517330 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517330' /scratch/stefan/7774842/working/building/REAL300004517330 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517330 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517330/0 /scratch/stefan/7774842/working/building/REAL300004517330 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 364) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/364 `/scratch/stefan/7774842/working/3D/364' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H](C(=O)NC2=CC=C3CCN(C)C3=C2)O[C@H]1C(=O)[O-]) `REAL300004517330.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517330.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517330/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517330 none C[C@@H]1C[C@H](C(=O)NC2=CC=C3CCN(C)C3=C2)O[C@H]1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 12, 5, 7, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 9, 28, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 9, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1] 28 rigid atoms, others: [32, 33, 34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 40, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39]) total number of confs: 77 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517330 none C[C@@H]1C[C@H](C(=O)NC2=CC=C3CCN(C)C3=C2)O[C@H]1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 12, 5, 7, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 9, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28] 28 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 19, 20, 21, 22, 28, 29] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 55 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517330 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517330 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517330/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517330 Building REAL300004517331 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517331' /scratch/stefan/7774842/working/building/REAL300004517331 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517331 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517331/0 /scratch/stefan/7774842/working/building/REAL300004517331 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 365) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/365 `/scratch/stefan/7774842/working/3D/365' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)C3=CC=C(CC(=O)[O-])C=C3)C=C21) `REAL300004517331.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517331.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517331/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517331 none CN1CCC2=CC=C(NC(=O)C3=CC=C(CC(=O)[O-])C=C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 3, 3, 1, 3, 1, 1, 1, 1, 1, 3, 3, 3, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 1, 1, 3, 3, 1, 1, 9] 13 rigid atoms, others: [33, 34, 37, 38, 9, 11, 12, 13, 14, 15, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 39]) total number of confs: 24 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517331 none CN1CCC2=CC=C(NC(=O)C3=CC=C(CC(=O)[O-])C=C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 5, 5, 13, 13, 13, 9, 9, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 5, 9, 9, 13, 13, 9, 9, 1] 13 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 39, 21, 22, 26, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 73 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517331 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517331 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517331/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517331 Building REAL300004517332 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517332' /scratch/stefan/7774842/working/building/REAL300004517332 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517332 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517332/0 /scratch/stefan/7774842/working/building/REAL300004517332 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 366) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/366 `/scratch/stefan/7774842/working/3D/366' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)C3=CC=C(C=CC(=O)[O-])C=C3)C=C21) `REAL300004517332.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517332.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517332/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517332 none CN1CCC2=CC=C(NC(=O)C3=CC=C(C=CC(=O)[O-])C=C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [15, 15, 15, 15, 15, 15, 15, 4, 4, 1, 4, 1, 1, 1, 1, 1, 6, 6, 13, 13, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 4, 1, 1, 6, 6, 1, 1, 15] 27 rigid atoms, others: [34, 35, 38, 39, 9, 11, 12, 13, 14, 15, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 40]) total number of confs: 57 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517332 none CN1CCC2=CC=C(NC(=O)C3=CC=C(C=CC(=O)[O-])C=C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 15, 15, 9, 15, 27, 27, 27, 27, 15, 15, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 9, 15, 15, 27, 27, 15, 15, 1] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 40, 32, 22, 23, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 107 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517332 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517332 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517332/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517332 Building REAL300004517333 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517333' /scratch/stefan/7774842/working/building/REAL300004517333 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517333 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517333/0 /scratch/stefan/7774842/working/building/REAL300004517333 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 367) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/367 `/scratch/stefan/7774842/working/3D/367' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)C=CC3=CC(C(=O)[O-])=CO3)C=C21) `REAL300004517333.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517333.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517333/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517333 none CN1CCC2=CC=C(NC(=O)C=CC3=CC(C(=O)[O-])=CO3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 54, 54, 54, 54, 54, 30, 30, 9, 30, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 30, 9, 9, 1, 1, 54] 54 rigid atoms, others: [35, 36, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37]) total number of confs: 115 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517333 none CN1CCC2=CC=C(NC(=O)C=CC3=CC(C(=O)[O-])=CO3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 31, 31, 54, 54, 54, 54, 54, 54, 54, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 9, 31, 31, 54, 54, 1] 54 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 37, 21, 22, 26, 27, 28, 29, 30, 31] set([32, 33, 34, 35, 36, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517333 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517333 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517333/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517333 Building REAL300004517334 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517334' /scratch/stefan/7774842/working/building/REAL300004517334 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517334 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517334/0 /scratch/stefan/7774842/working/building/REAL300004517334 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 368) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/368 `/scratch/stefan/7774842/working/3D/368' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)C3=CC=CC=C3CCC(=O)[O-])C=C21) `REAL300004517334.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517334.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517334/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517334 none CN1CCC2=CC=C(NC(=O)C3=CC=CC=C3CCC(=O)[O-])C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 43, 43, 43, 43, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 5, 9, 17, 16, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 43, 7, 1, 1, 1, 1, 5, 5, 9, 9, 43] 89 rigid atoms, others: [34, 35, 36, 37, 9, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 121 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517334 none CN1CCC2=CC=C(NC(=O)C3=CC=CC=C3CCC(=O)[O-])C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 43, 43, 43, 43, 43, 43, 73, 89, 89, 89, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 9, 43, 43, 43, 43, 73, 73, 89, 89, 1] 89 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 42, 32, 22, 23, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 328 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517334 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517334 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517334/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517334 Building REAL300004517335 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517335' /scratch/stefan/7774842/working/building/REAL300004517335 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517335 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517335/0 /scratch/stefan/7774842/working/building/REAL300004517335 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 369) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/369 `/scratch/stefan/7774842/working/3D/369' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)COCC3=C(C(=O)[O-])N=CO3)C=C21) `REAL300004517335.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517335.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517335/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517335 none CN1CCC2=CC=C(NC(=O)COCC3=C(C(=O)[O-])N=CO3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 1, 11, 11, 8, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 116, 116, 72, 116, 28, 6, 1, 1, 1, 1, 2, 2, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 116, 72, 72, 6, 6, 1, 201] 201 rigid atoms, others: [38, 13, 14, 15, 16, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39]) total number of confs: 528 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517335 none CN1CCC2=CC=C(NC(=O)COCC3=C(C(=O)[O-])N=CO3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 1, 11, 11, 8, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 28, 75, 152, 201, 201, 201, 201, 201, 201, 201, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 9, 32, 32, 152, 152, 201, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 39, 32, 22, 23, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 33, 34, 35, 36, 37, 38]) total number of confs: 604 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517335 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517335 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517335/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517335 Building REAL300004517336 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517336' /scratch/stefan/7774842/working/building/REAL300004517336 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517336 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517336/0 /scratch/stefan/7774842/working/building/REAL300004517336 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 370) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/370 `/scratch/stefan/7774842/working/3D/370' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)C=CC3=CC=C(C(=O)[O-])O3)C=C21) `REAL300004517336.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517336/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517336 none CN1CCC2=CC=C(NC(=O)C=CC3=CC=C(C(=O)[O-])O3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 47, 47, 47, 47, 27, 27, 10, 27, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 27, 10, 10, 1, 1, 47] 47 rigid atoms, others: [35, 36, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37]) total number of confs: 103 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517336 none CN1CCC2=CC=C(NC(=O)C=CC3=CC=C(C(=O)[O-])O3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 26, 26, 47, 47, 47, 47, 47, 47, 47, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 9, 26, 26, 47, 47, 1] 47 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 37, 21, 22, 26, 27, 28, 29, 30, 31] set([32, 33, 34, 35, 36, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25]) total number of confs: 106 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517336 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517336 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517336/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517336 Building REAL300004517337 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517337' /scratch/stefan/7774842/working/building/REAL300004517337 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517337 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517337/0 /scratch/stefan/7774842/working/building/REAL300004517337 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 371) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/371 `/scratch/stefan/7774842/working/3D/371' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)NC2=CC=C3CCN(C)C3=C2)C=C1C(=O)[O-]) `REAL300004517337.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517337.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517337/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517337 none CC1=CC=C(C(=O)NC2=CC=C3CCN(C)C3=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [25, 25, 25, 25, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 8, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 25] 25 rigid atoms, others: [32, 33, 34, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 35, 36, 37, 39]) total number of confs: 47 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517337 none CC1=CC=C(C(=O)NC2=CC=C3CCN(C)C3=C2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 5, 5, 5, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 5, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1] 25 rigid atoms, others: [0, 1, 2, 3, 4, 5, 39, 18, 19, 20, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517337 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517337 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517337/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517337 Building REAL300004517338 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517338' /scratch/stefan/7774842/working/building/REAL300004517338 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517338 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517338/0 /scratch/stefan/7774842/working/building/REAL300004517338 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 372) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/372 `/scratch/stefan/7774842/working/3D/372' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=C(C(=O)[O-])C=C1C(=O)NC1=CC=C2CCN(C)C2=C1) `REAL300004517338.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517338.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517338/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517338 none CC1=NC=C(C(=O)[O-])C=C1C(=O)NC1=CC=C2CCN(C)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 11, 8, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 20, 20, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 9, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1] 20 rigid atoms, others: [32, 33, 34, 38, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 35, 23, 24, 25, 26, 27, 28, 37, 36]) total number of confs: 43 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517338 none CC1=NC=C(C(=O)[O-])C=C1C(=O)NC1=CC=C2CCN(C)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 11, 8, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 20, 20, 20, 20, 20, 20, 20, 20, 20, 2, 2, 2, 1, 1, 8, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20] 20 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517338 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517338 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517338/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517338 Building REAL300004517339 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517339' /scratch/stefan/7774842/working/building/REAL300004517339 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517339 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517339/0 /scratch/stefan/7774842/working/building/REAL300004517339 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 373) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/373 `/scratch/stefan/7774842/working/3D/373' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)CN3C=CC(C(=O)[O-])=N3)C=C21) `REAL300004517339.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517339 none CN1CCC2=CC=C(NC(=O)CN3C=CC(C(=O)[O-])=N3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 8, 1, 1, 1, 1, 11, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 77, 77, 77, 77, 77, 33, 33, 9, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 77, 77, 77, 77, 77, 77, 77, 77, 77, 77, 77, 33, 9, 9, 1, 1, 77] 77 rigid atoms, others: [34, 35, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 158 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517339 none CN1CCC2=CC=C(NC(=O)CN3C=CC(C(=O)[O-])=N3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 8, 1, 1, 1, 1, 11, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 50, 77, 77, 77, 77, 77, 77, 77, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 77, 77, 1] 77 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 25, 26, 27, 28, 29, 30, 36] set([32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 31]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517339 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517339 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517339/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517339 Building REAL300004517340 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517340' /scratch/stefan/7774842/working/building/REAL300004517340 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517340 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517340/0 /scratch/stefan/7774842/working/building/REAL300004517340 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 374) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/374 `/scratch/stefan/7774842/working/3D/374' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)CCCN3C=CC(C(=O)[O-])=N3)C=C21) `REAL300004517340.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517340/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517340 none CN1CCC2=CC=C(NC(=O)CCCN3C=CC(C(=O)[O-])=N3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 1, 11, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 136 conformations in input total number of sets (complete confs): 136 using faster count positions algorithm for large data unique positions, atoms: [136, 136, 136, 136, 136, 136, 136, 57, 57, 29, 57, 14, 8, 1, 1, 1, 1, 1, 1, 2, 2, 1, 136, 136, 136, 136, 136, 136, 136, 136, 136, 136, 136, 57, 29, 29, 14, 14, 8, 8, 1, 1, 136] 136 rigid atoms, others: [40, 41, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42]) total number of confs: 348 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517340 none CN1CCC2=CC=C(NC(=O)CCCN3C=CC(C(=O)[O-])=N3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 1, 11, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 136 conformations in input total number of sets (complete confs): 136 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 47, 60, 77, 136, 136, 136, 136, 136, 136, 136, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 9, 47, 47, 69, 69, 72, 73, 136, 136, 1] 136 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 42, 32, 22, 23, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 461 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517340 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517340 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517340/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517340 Building REAL300004517341 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517341' /scratch/stefan/7774842/working/building/REAL300004517341 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517341 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517341/0 /scratch/stefan/7774842/working/building/REAL300004517341 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 375) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/375 `/scratch/stefan/7774842/working/3D/375' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)[C@H]3CC[C@@H](CCC(=O)[O-])O3)C=C21) `REAL300004517341.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517341/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517341 none CN1CCC2=CC=C(NC(=O)[C@H]3CC[C@@H](CCC(=O)[O-])O3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 5, 5, 7, 5, 5, 1, 11, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 48, 48, 48, 48, 48, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 8, 18, 30, 30, 1, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 10, 1, 1, 1, 1, 8, 8, 18, 18, 48] 127 rigid atoms, others: [35, 36, 37, 38, 9, 11, 12, 13, 14, 15, 16, 17, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 18, 19, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43]) total number of confs: 182 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517341 none CN1CCC2=CC=C(NC(=O)[C@H]3CC[C@@H](CCC(=O)[O-])O3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 5, 5, 7, 5, 5, 1, 11, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 48, 48, 48, 48, 48, 48, 109, 127, 127, 127, 48, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 11, 48, 48, 48, 48, 109, 109, 127, 127, 1] 127 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 7, 43, 23, 24, 33, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 476 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517341 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517341 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517341/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517341 Building REAL300004517342 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517342' /scratch/stefan/7774842/working/building/REAL300004517342 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517342 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517342/0 /scratch/stefan/7774842/working/building/REAL300004517342 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 376) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/376 `/scratch/stefan/7774842/working/3D/376' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)CC[C@@H]3C[C@H](C(=O)[O-])CO3)C=C21) `REAL300004517342.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517342 none CN1CCC2=CC=C(NC(=O)CC[C@@H]3C[C@H](C(=O)[O-])CO3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 7, 5, 5, 7, 1, 11, 11, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 186 conformations in input total number of sets (complete confs): 186 using faster count positions algorithm for large data unique positions, atoms: [186, 186, 186, 186, 186, 186, 186, 66, 66, 15, 66, 8, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 186, 186, 186, 186, 186, 186, 186, 186, 186, 186, 186, 66, 15, 15, 8, 8, 1, 1, 1, 1, 186] 186 rigid atoms, others: [39, 40, 41, 42, 12, 13, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43]) total number of confs: 358 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517342 none CN1CCC2=CC=C(NC(=O)CC[C@@H]3C[C@H](C(=O)[O-])CO3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 7, 5, 5, 7, 1, 11, 11, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 186 conformations in input total number of sets (complete confs): 186 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 69, 101, 186, 186, 186, 186, 186, 186, 186, 186, 186, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 11, 69, 69, 117, 117, 186, 186, 186, 186, 1] 186 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 7, 43, 23, 24, 33, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 762 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517342 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517342 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517342/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517342 Building REAL300004517343 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517343' /scratch/stefan/7774842/working/building/REAL300004517343 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517343 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517343/0 /scratch/stefan/7774842/working/building/REAL300004517343 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 377) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/377 `/scratch/stefan/7774842/working/3D/377' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2=CC=C3CCN(C)C3=C2)OC(C(=O)[O-])=C1) `REAL300004517343.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517343.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517343/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517343 none CC1=C(C(=O)NC2=CC=C3CCN(C)C3=C2)OC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 12, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 8, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 15] 15 rigid atoms, others: [35, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 33, 32, 34, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 36]) total number of confs: 34 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517343 none CC1=C(C(=O)NC2=CC=C3CCN(C)C3=C2)OC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 12, 1, 1, 11, 11, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 9, 9, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 2, 2, 1, 2, 2, 2, 10, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1] 15 rigid atoms, others: [0, 1, 2, 3, 36, 16, 17, 18, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517343 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517343 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517343/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517343 Building REAL300004517344 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517344' /scratch/stefan/7774842/working/building/REAL300004517344 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517344 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517344/0 /scratch/stefan/7774842/working/building/REAL300004517344 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 378) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/378 `/scratch/stefan/7774842/working/3D/378' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)[C@@H]3C4C=CC(CC4)[C@@H]3C(=O)[O-])C=C21) `REAL300004517344.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517344.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517344/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517344 none CN1CCC2=CC=C(NC(=O)[C@@H]3C4C=CC(CC4)[C@@H]3C(=O)[O-])C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 1, 1, 5, 5, 5, 5, 7, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 8, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 1, 1, 1, 1, 1, 1, 1, 1, 8] 8 rigid atoms, others: [43, 36, 37, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 44]) total number of confs: 17 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517344 none CN1CCC2=CC=C(NC(=O)[C@@H]3C4C=CC(CC4)[C@@H]3C(=O)[O-])C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 1, 1, 5, 5, 5, 5, 7, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 7, 8, 8, 8, 8, 8, 8, 8, 8, 1] 8 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 7, 44, 34, 24, 25, 33, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 25 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517344 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517344 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517344/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517344 Building REAL300004517345 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517345' /scratch/stefan/7774842/working/building/REAL300004517345 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517345 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517345/0 /scratch/stefan/7774842/working/building/REAL300004517345 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 379) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/379 `/scratch/stefan/7774842/working/3D/379' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)[C@H]3CCCC[C@H]3C(=O)[O-])C=C21) `REAL300004517345.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517345/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517345 none CN1CCC2=CC=C(NC(=O)[C@H]3CCCC[C@H]3C(=O)[O-])C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 5, 5, 5, 5, 7, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 7] 7 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 42]) total number of confs: 15 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517345 none CN1CCC2=CC=C(NC(=O)[C@H]3CCCC[C@H]3C(=O)[O-])C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 5, 5, 5, 5, 7, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1] 7 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 42, 32, 22, 23, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 21 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517345 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517345 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517345/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517345 Building REAL300004517346 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517346' /scratch/stefan/7774842/working/building/REAL300004517346 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300004517346 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517346/0 /scratch/stefan/7774842/working/building/REAL300004517346 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 380) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/380 `/scratch/stefan/7774842/working/3D/380' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)C[N@@H+]3CCCC(C(=O)[O-])C3)C=C21) `REAL300004517346.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517346/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517346 none CN1CCC2=CC=C(NC(=O)C[N@@H+]3CCCC(C(=O)[O-])C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 1, 11, 11, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 63, 63, 63, 63, 16, 16, 5, 16, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 63, 63, 63, 63, 63, 63, 63, 63, 63, 63, 63, 16, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 63] 63 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 18, 21, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45]) total number of confs: 113 number of broken/clashed sets: 63 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517346 none CN1CCC2=CC=C(NC(=O)C[N@@H+]3CCCC(C(=O)[O-])C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 1, 11, 11, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 63 conformations in input total number of sets (complete confs): 63 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 35, 63, 63, 63, 63, 63, 63, 63, 63, 63, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 9, 35, 35, 63, 63, 63, 63, 63, 63, 63, 63, 63, 1] 63 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 45, 32, 22, 23, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 225 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517346 /scratch/stefan/7774842/working /scratch/stefan/7774842 mkdir: created directory `1' /scratch/stefan/7774842/working/building/REAL300004517346/1 /scratch/stefan/7774842/working/building/REAL300004517346 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 1 (index: 381) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/381 `/scratch/stefan/7774842/working/3D/381' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)C[N@H+]3CCCC(C(=O)[O-])C3)C=C21) `REAL300004517346.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004517346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517346/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517346 none CN1CCC2=CC=C(NC(=O)C[N@H+]3CCCC(C(=O)[O-])C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 1, 11, 11, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [99, 99, 99, 99, 99, 99, 99, 31, 31, 10, 31, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 99, 99, 99, 99, 99, 99, 99, 99, 99, 99, 99, 31, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 99] 99 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 18, 21, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45]) total number of confs: 189 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517346 none CN1CCC2=CC=C(NC(=O)C[N@H+]3CCCC(C(=O)[O-])C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 1, 11, 11, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 63, 99, 99, 99, 99, 99, 99, 99, 99, 99, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 9, 63, 63, 99, 99, 99, 99, 99, 99, 99, 99, 99, 1] 99 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 45, 32, 22, 23, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 323 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517346 /scratch/stefan/7774842/working /scratch/stefan/7774842 mkdir: created directory `2' /scratch/stefan/7774842/working/building/REAL300004517346/2 /scratch/stefan/7774842/working/building/REAL300004517346 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 2 (index: 382) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/382 `/scratch/stefan/7774842/working/3D/382' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)CN3CCCC(C(=O)[O-])C3)C=C21) `REAL300004517346.mol2' -> `2.mol2' `temp.mol2' -> `REAL300004517346.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517346/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517346 none CN1CCC2=CC=C(NC(=O)CN3CCCC(C(=O)[O-])C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 10, 5, 5, 5, 5, 1, 11, 11, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [72, 72, 72, 72, 72, 72, 72, 25, 25, 10, 25, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 72, 72, 72, 72, 72, 72, 72, 72, 72, 72, 72, 25, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 72] 72 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 20, 43] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44]) total number of confs: 139 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517346 none CN1CCC2=CC=C(NC(=O)CN3CCCC(C(=O)[O-])C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 10, 5, 5, 5, 5, 1, 11, 11, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 48, 72, 72, 72, 72, 72, 72, 72, 72, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 9, 48, 48, 72, 72, 72, 72, 72, 72, 72, 72, 72, 1] 72 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 44, 21, 22, 26, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517346 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517346 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 2: /scratch/stefan/7774842/working/building/REAL300004517346/2.* 1: /scratch/stefan/7774842/working/building/REAL300004517346/1.* 0: /scratch/stefan/7774842/working/building/REAL300004517346/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517346 Building REAL300004517347 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517347' /scratch/stefan/7774842/working/building/REAL300004517347 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517347 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517347/0 /scratch/stefan/7774842/working/building/REAL300004517347 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 383) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/383 `/scratch/stefan/7774842/working/3D/383' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)C3(C(=O)[O-])CC3C3=CC=CC=C3)C=C21) `REAL300004517347.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517347.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517347/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517347 none CN1CCC2=CC=C(NC(=O)C3(C(=O)[O-])CC3C3=CC=CC=C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 1, 11, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 5, 4, 1, 4, 1, 1, 3, 3, 1, 1, 1, 2, 2, 2, 2, 2, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 5, 1, 1, 1, 2, 2, 2, 2, 2, 23] 23 rigid atoms, others: [35, 36, 37, 9, 11, 12, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43]) total number of confs: 43 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517347 none CN1CCC2=CC=C(NC(=O)C3(C(=O)[O-])CC3C3=CC=CC=C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 1, 11, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 9, 23, 23, 23, 23, 23, 23, 23, 23, 1] 23 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 7, 43, 23, 24, 33, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 69 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517347 none CN1CCC2=CC=C(NC(=O)C3(C(=O)[O-])CC3C3=CC=CC=C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 1, 11, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 5, 5, 2, 5, 2, 2, 3, 3, 2, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 5, 2, 2, 2, 1, 1, 1, 1, 1, 23] 23 rigid atoms, others: [38, 39, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43]) total number of confs: 39 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517347 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517347 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517347/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517347 Building REAL300004517348 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517348' /scratch/stefan/7774842/working/building/REAL300004517348 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517348 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517348/0 /scratch/stefan/7774842/working/building/REAL300004517348 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 384) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/384 `/scratch/stefan/7774842/working/3D/384' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)C3=C(CC(=O)[O-])C4=CC=CC=C4N3)C=C21) `REAL300004517348.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517348.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517348/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517348 none CN1CCC2=CC=C(NC(=O)C3=C(CC(=O)[O-])C4=CC=CC=C4N3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 15, 15, 15, 15, 15, 5, 5, 1, 5, 1, 1, 1, 2, 7, 7, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 5, 2, 2, 1, 1, 1, 1, 1, 15] 15 rigid atoms, others: [38, 39, 40, 9, 41, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43]) total number of confs: 45 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517348 none CN1CCC2=CC=C(NC(=O)C3=C(CC(=O)[O-])C4=CC=CC=C4N3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 7, 15, 15, 15, 15, 15, 15, 15, 1] 15 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 7, 34, 43, 24, 25, 33, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 33 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517348 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517348 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517348/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517348 Building REAL300004517349 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517349' /scratch/stefan/7774842/working/building/REAL300004517349 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517349 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517349/0 /scratch/stefan/7774842/working/building/REAL300004517349 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 385) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/385 `/scratch/stefan/7774842/working/3D/385' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)CN3C=C(C(=O)[O-])C4=CC=CC=C43)C=C21) `REAL300004517349.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517349 none CN1CCC2=CC=C(NC(=O)CN3C=C(C(=O)[O-])C4=CC=CC=C43)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [100, 100, 100, 100, 100, 100, 100, 36, 36, 8, 36, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 36, 8, 8, 1, 1, 1, 1, 1, 100] 100 rigid atoms, others: [38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 43]) total number of confs: 192 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517349 none CN1CCC2=CC=C(NC(=O)CN3C=C(C(=O)[O-])C4=CC=CC=C43)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 56, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 100, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 9, 56, 56, 100, 100, 100, 100, 100, 1] 100 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 7, 34, 43, 24, 25, 33, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 265 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517349 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517349 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517349/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517349 Building REAL300004517350 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517350' /scratch/stefan/7774842/working/building/REAL300004517350 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517350 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517350/0 /scratch/stefan/7774842/working/building/REAL300004517350 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 386) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/386 `/scratch/stefan/7774842/working/3D/386' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)C3CC4(CC4C(=O)[O-])C3)C=C21) `REAL300004517350.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517350.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517350/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517350 none CN1CCC2=CC=C(NC(=O)C3CC4(CC4C(=O)[O-])C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 40, 40, 40, 12, 12, 1, 12, 1, 1, 1, 1, 1, 1, 3, 3, 1, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 12, 1, 1, 1, 1, 1, 1, 1, 1, 40] 40 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 9, 11, 12, 13, 14, 15, 16, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 40]) total number of confs: 67 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517350 none CN1CCC2=CC=C(NC(=O)C3CC4(CC4C(=O)[O-])C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 10, 40, 40, 40, 40, 40, 40, 40, 40, 1] 40 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 40, 20, 21, 25, 26, 27, 28, 29, 30] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 101 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517350 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517350 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517350/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517350 Building REAL300004517351 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517351' /scratch/stefan/7774842/working/building/REAL300004517351 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517351 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517351/0 /scratch/stefan/7774842/working/building/REAL300004517351 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 387) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/387 `/scratch/stefan/7774842/working/3D/387' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@]1(C(=O)[O-])C[C@@H]1C(=O)NC1=CC=C2CCN(C)C2=C1) `REAL300004517351.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517351.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517351/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517351 none CC(C)[C@@]1(C(=O)[O-])C[C@@H]1C(=O)NC1=CC=C2CCN(C)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 14, 15, 14, 14, 14, 14, 14, 9, 14, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 14, 14, 9, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1] 15 rigid atoms, others: [33, 34, 35, 36, 37, 38, 42, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41]) total number of confs: 51 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517351 none CC(C)[C@@]1(C(=O)[O-])C[C@@H]1C(=O)NC1=CC=C2CCN(C)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 7, 1, 11, 8, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [4, 1, 4, 1, 1, 2, 2, 1, 1, 1, 1, 5, 5, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 4, 4, 4, 4, 4, 4, 1, 1, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14] 15 rigid atoms, others: [1, 3, 4, 7, 8, 9, 10, 30, 31] set([0, 2, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517351 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517351 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517351/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517351 Building REAL300004517352 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517352' /scratch/stefan/7774842/working/building/REAL300004517352 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517352 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517352/0 /scratch/stefan/7774842/working/building/REAL300004517352 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 388) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/388 `/scratch/stefan/7774842/working/3D/388' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)[O-])C=C1C(=O)NC1=CC=C2CCN(C)C2=C1) `REAL300004517352.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517352 none CC1=CC=C(C(=O)[O-])C=C1C(=O)NC1=CC=C2CCN(C)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 8, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 20, 20, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 9, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1] 20 rigid atoms, others: [32, 33, 34, 35, 39, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 36, 37, 38]) total number of confs: 43 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517352 none CC1=CC=C(C(=O)[O-])C=C1C(=O)NC1=CC=C2CCN(C)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 8, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 2, 2, 2, 1, 1, 1, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20] 20 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517352 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517352 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517352/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517352 Building REAL300004517353 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517353' /scratch/stefan/7774842/working/building/REAL300004517353 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517353 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517353/0 /scratch/stefan/7774842/working/building/REAL300004517353 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 389) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/389 `/scratch/stefan/7774842/working/3D/389' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)C3=C(C(=O)[O-])SC=C3)C=C21) `REAL300004517353.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517353/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517353 none CN1CCC2=CC=C(NC(=O)C3=C(C(=O)[O-])SC=C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 11, 11, 14, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 5, 5, 1, 5, 1, 1, 1, 3, 3, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 5, 1, 1, 21] 21 rigid atoms, others: [32, 9, 11, 12, 13, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 37 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517353 none CN1CCC2=CC=C(NC(=O)C3=C(C(=O)[O-])SC=C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 11, 11, 14, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 21, 21, 21, 21, 21, 21, 21, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 9, 21, 21, 1] 21 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 33, 19, 20, 24, 25, 26, 27, 28, 29] set([32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 30, 31]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517353 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517353 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517353/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517353 Building REAL300004517354 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517354' /scratch/stefan/7774842/working/building/REAL300004517354 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517354 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517354/0 /scratch/stefan/7774842/working/building/REAL300004517354 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 390) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/390 `/scratch/stefan/7774842/working/3D/390' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=NC=C1C(=O)NC1=CC=C2CCN(C)C2=C1) `REAL300004517354.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517354 none CC1=C(C(=O)[O-])C=NC=C1C(=O)NC1=CC=C2CCN(C)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 8, 1, 1, 1, 11, 8, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 19, 19, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 9, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1] 19 rigid atoms, others: [32, 33, 34, 38, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 35, 23, 24, 25, 26, 27, 28, 37, 36]) total number of confs: 41 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517354 none CC1=C(C(=O)[O-])C=NC=C1C(=O)NC1=CC=C2CCN(C)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 8, 1, 1, 1, 11, 8, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 7, 7, 7, 19, 19, 19, 19, 19, 19, 19, 19, 19, 2, 2, 2, 1, 1, 7, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19] 19 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 9, 10, 26, 27] set([4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517354 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517354 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517354/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517354 Building REAL300004517355 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517355' /scratch/stefan/7774842/working/building/REAL300004517355 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517355 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517355/0 /scratch/stefan/7774842/working/building/REAL300004517355 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 391) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/391 `/scratch/stefan/7774842/working/3D/391' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1C(=O)NC1=CC=C2CCN(C)C2=C1) `REAL300004517355.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517355.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517355/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517355 none CC1=CC(C(=O)[O-])=CC=C1C(=O)NC1=CC=C2CCN(C)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1] 17 rigid atoms, others: [32, 33, 34, 35, 39, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 36, 37, 38]) total number of confs: 37 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517355 none CC1=CC(C(=O)[O-])=CC=C1C(=O)NC1=CC=C2CCN(C)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 2, 2, 2, 1, 1, 1, 7, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517355 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517355 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517355/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517355 Building REAL300004517356 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517356' /scratch/stefan/7774842/working/building/REAL300004517356 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517356 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517356/0 /scratch/stefan/7774842/working/building/REAL300004517356 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 392) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/392 `/scratch/stefan/7774842/working/3D/392' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)C3=CC=C(C(=O)[O-])C=C3Cl)C=C21) `REAL300004517356.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517356/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517356 none CN1CCC2=CC=C(NC(=O)C3=CC=C(C(=O)[O-])C=C3Cl)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 5, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 5, 1, 1, 1, 13] 13 rigid atoms, others: [33, 34, 35, 9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36]) total number of confs: 23 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517356 none CN1CCC2=CC=C(NC(=O)C3=CC=C(C(=O)[O-])C=C3Cl)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 5, 13, 13, 13, 1] 13 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 21, 22, 36, 26, 27, 28, 29, 30, 31] set([32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25]) total number of confs: 29 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517356 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517356 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517356/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517356 Building REAL300004517357 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517357' /scratch/stefan/7774842/working/building/REAL300004517357 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517357 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517357/0 /scratch/stefan/7774842/working/building/REAL300004517357 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 393) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/393 `/scratch/stefan/7774842/working/3D/393' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)C3CC4(CC(C(=O)[O-])C4)C3)C=C21) `REAL300004517357.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517357 none CN1CCC2=CC=C(NC(=O)C3CC4(CC(C(=O)[O-])C4)C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28] 28 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 19, 20, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 43]) total number of confs: 49 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517357 none CN1CCC2=CC=C(NC(=O)C3CC4(CC(C(=O)[O-])C4)C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 10, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1] 28 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 43, 21, 22, 26, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517357 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517357 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517357/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517357 Building REAL300004517358 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517358' /scratch/stefan/7774842/working/building/REAL300004517358 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517358 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517358/0 /scratch/stefan/7774842/working/building/REAL300004517358 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 394) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/394 `/scratch/stefan/7774842/working/3D/394' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)[O-])=NC(C(=O)NC2=CC=C3CCN(C)C3=C2)=C1) `REAL300004517358.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517358/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517358 none COC1=CC(C(=O)[O-])=NC(C(=O)NC2=CC=C3CCN(C)C3=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 8, 1, 1, 11, 8, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 13, 13, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 9, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 13] 13 rigid atoms, others: [32, 33, 34, 38, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 35, 36, 37, 39]) total number of confs: 33 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517358 none COC1=CC(C(=O)[O-])=NC(C(=O)NC2=CC=C3CCN(C)C3=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 8, 1, 1, 11, 8, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 3, 3, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 3, 3, 3, 1, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1] 13 rigid atoms, others: [1, 2, 3, 4, 5, 39, 8, 9, 10, 23, 27] set([0, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 30 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517358 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517358 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517358/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517358 Building REAL300004517359 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517359' /scratch/stefan/7774842/working/building/REAL300004517359 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517359 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517359/0 /scratch/stefan/7774842/working/building/REAL300004517359 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 395) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/395 `/scratch/stefan/7774842/working/3D/395' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)C3=CC=C(CCC(=O)[O-])C=C3)C=C21) `REAL300004517359.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517359/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517359 none CN1CCC2=CC=C(NC(=O)C3=CC=C(CCC(=O)[O-])C=C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 5, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 3, 3, 1, 3, 1, 1, 1, 1, 1, 8, 14, 21, 17, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 3, 1, 1, 8, 8, 14, 14, 1, 1, 16] 65 rigid atoms, others: [34, 35, 40, 9, 11, 12, 13, 14, 15, 20, 21, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 42]) total number of confs: 98 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517359 none CN1CCC2=CC=C(NC(=O)C3=CC=C(CCC(=O)[O-])C=C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 5, 5, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 64 conformations in input total number of sets (complete confs): 64 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 15, 15, 9, 9, 40, 64, 64, 60, 15, 15, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 9, 15, 15, 40, 40, 64, 64, 15, 15, 1] 64 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 42, 32, 22, 23, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 284 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517359 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517359 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517359/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517359 Building REAL300004517360 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517360' /scratch/stefan/7774842/working/building/REAL300004517360 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517360 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517360/0 /scratch/stefan/7774842/working/building/REAL300004517360 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 396) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/396 `/scratch/stefan/7774842/working/3D/396' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C(C(=O)NC2=CC=C3CCN(C)C3=C2)=NN1) `REAL300004517360.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517360.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517360/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517360 none CC1=C(C(=O)[O-])C(C(=O)NC2=CC=C3CCN(C)C3=C2)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 11, 8, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 7, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 13] 13 rigid atoms, others: [35, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 34, 20, 21, 22, 23, 24, 25, 33, 36]) total number of confs: 31 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517360 none CC1=C(C(=O)[O-])C(C(=O)NC2=CC=C3CCN(C)C3=C2)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 11, 8, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 8, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 4, 4, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 2, 2, 2, 4, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1] 13 rigid atoms, others: [0, 1, 2, 3, 36, 6, 7, 20, 21] set([4, 5, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 33 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517360 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517360 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517360/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517360 Building REAL300004517361 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517361' /scratch/stefan/7774842/working/building/REAL300004517361 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517361 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517361/0 /scratch/stefan/7774842/working/building/REAL300004517361 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 397) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/397 `/scratch/stefan/7774842/working/3D/397' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)C3CC4(C3)C(C(=O)[O-])C4(F)F)C=C21) `REAL300004517361.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517361.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517361/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517361 none CN1CCC2=CC=C(NC(=O)C3CC4(C3)C(C(=O)[O-])C4(F)F)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [40, 40, 40, 40, 40, 40, 40, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 13, 1, 1, 1, 1, 1, 1, 40] 40 rigid atoms, others: [34, 35, 36, 37, 38, 39, 9, 11, 12, 13, 14, 15, 16, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40]) total number of confs: 70 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517361 none CN1CCC2=CC=C(NC(=O)C3CC4(C3)C(C(=O)[O-])C4(F)F)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 15, 15, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 9, 40, 40, 40, 40, 40, 40, 1] 40 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 40, 32, 22, 23, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 99 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517361 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517361 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517361/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517361 Building REAL300004517362 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517362' /scratch/stefan/7774842/working/building/REAL300004517362 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517362 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517362/0 /scratch/stefan/7774842/working/building/REAL300004517362 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 398) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/398 `/scratch/stefan/7774842/working/3D/398' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)C3=CSC(C(=O)[O-])=N3)C=C21) `REAL300004517362.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517362/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517362 none CN1CCC2=CC=C(NC(=O)C3=CSC(C(=O)[O-])=N3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 14, 1, 1, 11, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 4, 3, 1, 3, 1, 1, 1, 1, 1, 2, 2, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 1, 7] 7 rigid atoms, others: [9, 11, 12, 13, 14, 15, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32]) total number of confs: 19 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517362 none CN1CCC2=CC=C(NC(=O)C3=CSC(C(=O)[O-])=N3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 14, 1, 1, 11, 11, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 7, 7, 1] 7 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 19, 20, 32, 24, 25, 26, 27, 28, 29] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 30, 31]) total number of confs: 21 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517362 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517362 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517362/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517362 Building REAL300004517363 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517363' /scratch/stefan/7774842/working/building/REAL300004517363 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517363 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517363/0 /scratch/stefan/7774842/working/building/REAL300004517363 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 399) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/399 `/scratch/stefan/7774842/working/3D/399' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)NC2=CC=C3CCN(C)C3=C2)C=C(C(=O)[O-])S1) `REAL300004517363.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517363/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517363 none CC1=C(C(=O)NC2=CC=C3CCN(C)C3=C2)C=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17, 9, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 17] 17 rigid atoms, others: [35, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 33, 32, 34, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 36]) total number of confs: 37 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517363 none CC1=C(C(=O)NC2=CC=C3CCN(C)C3=C2)C=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 1, 1, 1, 11, 11, 14, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 8, 8, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 2, 2, 1, 2, 2, 2, 8, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1] 17 rigid atoms, others: [0, 1, 2, 3, 36, 16, 17, 18, 21] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 41 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517363 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517363 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517363/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517363 Building REAL300004517364 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517364' /scratch/stefan/7774842/working/building/REAL300004517364 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517364 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517364/0 /scratch/stefan/7774842/working/building/REAL300004517364 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 400) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/400 `/scratch/stefan/7774842/working/3D/400' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)C3=CC4=C(SC(C(=O)[O-])=C4)S3)C=C21) `REAL300004517364.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517364.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517364/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517364 none CN1CCC2=CC=C(NC(=O)C3=CC4=C(SC(C(=O)[O-])=C4)S3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 14, 1, 1, 11, 11, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 11, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 11, 1, 1, 22] 22 rigid atoms, others: [34, 35, 9, 11, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 44 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517364 none CN1CCC2=CC=C(NC(=O)C3=CC4=C(SC(C(=O)[O-])=C4)S3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 14, 1, 1, 11, 11, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 9, 22, 22, 1] 22 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 32, 22, 23, 36, 27, 28, 29, 30, 31] set([33, 34, 35, 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 /scratch/stefan/7774842/working/building/REAL300004517364 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517364 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517364/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517364 Building REAL300004517365 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517365' /scratch/stefan/7774842/working/building/REAL300004517365 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517365 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517365/0 /scratch/stefan/7774842/working/building/REAL300004517365 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 401) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/401 `/scratch/stefan/7774842/working/3D/401' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)[O-])=C(Cl)C(C(=O)NC2=CC=C3CCN(C)C3=C2)=C1) `REAL300004517365.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517365.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517365/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517365 none COC1=CC(C(=O)[O-])=C(Cl)C(C(=O)NC2=CC=C3CCN(C)C3=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 16, 1, 1, 11, 8, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 26, 26, 26, 26, 26, 45, 45, 26, 26, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 45, 45, 45, 26, 9, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 26] 45 rigid atoms, others: [32, 33, 34, 35, 39, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 36, 37, 38, 40]) total number of confs: 163 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517365 none COC1=CC(C(=O)[O-])=C(Cl)C(C(=O)NC2=CC=C3CCN(C)C3=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 16, 1, 1, 11, 8, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 1, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 7, 7, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 2, 2, 2, 1, 7, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1] 45 rigid atoms, others: [1, 2, 3, 4, 5, 8, 9, 10, 11, 40, 24, 28] set([0, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517365 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517365 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517365/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517365 Building REAL300004517366 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517366' /scratch/stefan/7774842/working/building/REAL300004517366 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517366 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517366/0 /scratch/stefan/7774842/working/building/REAL300004517366 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 402) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/402 `/scratch/stefan/7774842/working/3D/402' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=CC(F)=C1C(=O)NC1=CC=C2CCN(C)C2=C1) `REAL300004517366.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517366 none CC1=C(C(=O)[O-])C=CC(F)=C1C(=O)NC1=CC=C2CCN(C)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 15, 1, 1, 11, 8, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 9, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1] 20 rigid atoms, others: [32, 33, 34, 35, 39, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 36, 37, 38]) total number of confs: 42 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517366 none CC1=C(C(=O)[O-])C=CC(F)=C1C(=O)NC1=CC=C2CCN(C)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 15, 1, 1, 11, 8, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 20, 20, 20, 20, 20, 20, 20, 20, 20, 2, 2, 2, 1, 1, 7, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20] 20 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 9, 10, 11, 27, 28] set([4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517366 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517366 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517366/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517366 Building REAL300004517367 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517367' /scratch/stefan/7774842/working/building/REAL300004517367 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517367 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517367/0 /scratch/stefan/7774842/working/building/REAL300004517367 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 403) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/403 `/scratch/stefan/7774842/working/3D/403' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)C3=CC4=C(C(=O)[O-])C=CC=C4S3)C=C21) `REAL300004517367.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517367.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517367/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517367 none CN1CCC2=CC=C(NC(=O)C3=CC4=C(C(=O)[O-])C=CC=C4S3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 34, 34, 34, 11, 11, 1, 11, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 11, 1, 1, 1, 1, 34] 34 rigid atoms, others: [35, 36, 37, 38, 9, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39]) total number of confs: 61 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517367 none CN1CCC2=CC=C(NC(=O)C3=CC4=C(C(=O)[O-])C=CC=C4S3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 9, 34, 34, 34, 34, 1] 34 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 7, 23, 24, 39, 33, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 34, 35, 36, 37, 38]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517367 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517367 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517367/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517367 Building REAL300004517368 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517368' /scratch/stefan/7774842/working/building/REAL300004517368 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517368 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517368/0 /scratch/stefan/7774842/working/building/REAL300004517368 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 404) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/404 `/scratch/stefan/7774842/working/3D/404' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)CCC3=CC=CN=C3C(=O)[O-])C=C21) `REAL300004517368.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517368/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517368 none CN1CCC2=CC=C(NC(=O)CCC3=CC=CN=C3C(=O)[O-])C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 59, 59, 59, 59, 25, 25, 9, 25, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 59, 59, 59, 59, 59, 59, 59, 59, 59, 59, 59, 25, 9, 9, 5, 5, 1, 1, 1, 59] 59 rigid atoms, others: [38, 39, 40, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41]) total number of confs: 138 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517368 none CN1CCC2=CC=C(NC(=O)CCC3=CC=CN=C3C(=O)[O-])C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 39, 53, 59, 59, 59, 59, 59, 59, 59, 59, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 9, 39, 39, 53, 53, 59, 59, 59, 1] 59 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 41, 32, 22, 23, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 235 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517368 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517368 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517368/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517368 Building REAL300004517369 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517369' /scratch/stefan/7774842/working/building/REAL300004517369 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517369 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517369/0 /scratch/stefan/7774842/working/building/REAL300004517369 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 405) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/405 `/scratch/stefan/7774842/working/3D/405' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)C34CC(C(=O)[O-])(C3)CO4)C=C21) `REAL300004517369.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517369 none CN1CCC2=CC=C(NC(=O)C34CC(C(=O)[O-])(C3)CO4)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 11, 11, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 36, 36, 36, 36, 7, 7, 1, 7, 1, 1, 1, 1, 3, 3, 1, 1, 1, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 7, 1, 1, 1, 1, 1, 1, 36] 36 rigid atoms, others: [32, 33, 34, 35, 36, 37, 9, 11, 12, 13, 14, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38]) total number of confs: 56 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517369 none CN1CCC2=CC=C(NC(=O)C34CC(C(=O)[O-])(C3)CO4)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 11, 11, 5, 5, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 36, 36, 36, 36, 36, 36, 36, 36, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 10, 36, 36, 36, 36, 36, 36, 1] 36 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 38, 20, 21, 25, 26, 27, 28, 29, 30] set([32, 33, 34, 35, 36, 37, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 31]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517369 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517369 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517369/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517369 Building REAL300004517370 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517370' /scratch/stefan/7774842/working/building/REAL300004517370 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517370 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517370/0 /scratch/stefan/7774842/working/building/REAL300004517370 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 406) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/406 `/scratch/stefan/7774842/working/3D/406' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)/C=C/C3=CC=C(C(=O)[O-])C=C3)C=C21) `REAL300004517370.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517370.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517370/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517370 none CN1CCC2=CC=C(NC(=O)/C=C/C3=CC=C(C(=O)[O-])C=C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 22, 22, 22, 22, 11, 11, 3, 11, 3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 11, 3, 3, 1, 1, 1, 1, 22] 22 rigid atoms, others: [36, 37, 38, 39, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40]) total number of confs: 48 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517370 none CN1CCC2=CC=C(NC(=O)/C=C/C3=CC=C(C(=O)[O-])C=C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 20, 20, 22, 22, 21, 21, 22, 22, 22, 22, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 8, 22, 22, 22, 22, 22, 22, 1] 22 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 40, 32, 22, 23, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 78 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517370 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517370 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517370/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517370 Building REAL300004517371 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517371' /scratch/stefan/7774842/working/building/REAL300004517371 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517371 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517371/0 /scratch/stefan/7774842/working/building/REAL300004517371 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 407) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/407 `/scratch/stefan/7774842/working/3D/407' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)C3(C(=O)[O-])CC4(CCC4)C3)C=C21) `REAL300004517371.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517371.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517371/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517371 none CN1CCC2=CC=C(NC(=O)C3(C(=O)[O-])CC4(CCC4)C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 1, 11, 11, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 21, 21, 21, 21, 21, 21, 5, 5, 1, 5, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21] 21 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 9, 42, 11, 12, 15, 16, 17, 18, 19, 20, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 43]) total number of confs: 37 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517371 none CN1CCC2=CC=C(NC(=O)C3(C(=O)[O-])CC4(CCC4)C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 1, 11, 11, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 9, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1] 21 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 43, 21, 22, 26, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517371 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517371 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517371/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517371 Building REAL300004517372 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517372' /scratch/stefan/7774842/working/building/REAL300004517372 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517372 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517372/0 /scratch/stefan/7774842/working/building/REAL300004517372 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 408) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/408 `/scratch/stefan/7774842/working/3D/408' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)C3=C(C(=O)[O-])C=NN3C)C=C21) `REAL300004517372.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517372.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517372/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517372 none CN1CCC2=CC=C(NC(=O)C3=C(C(=O)[O-])C=NN3C)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 11, 11, 1, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 18, 18, 18, 18, 6, 6, 1, 6, 1, 1, 1, 3, 3, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 1, 2, 2, 2, 18] 18 rigid atoms, others: [32, 9, 11, 12, 13, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36]) total number of confs: 41 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517372 none CN1CCC2=CC=C(NC(=O)C3=C(C(=O)[O-])C=NN3C)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 11, 11, 1, 8, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 18 conformations in input total number of sets (complete confs): 18 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 9, 18, 18, 18, 18, 1] 18 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 25, 26, 27, 28, 29, 30, 36] set([32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 31]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517372 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517372 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517372/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517372 Building REAL300004517373 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517373' /scratch/stefan/7774842/working/building/REAL300004517373 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517373 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517373/0 /scratch/stefan/7774842/working/building/REAL300004517373 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 409) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/409 `/scratch/stefan/7774842/working/3D/409' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)C3=CC4=C(N3)C(C(=O)[O-])=CS4)C=C21) `REAL300004517373.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517373 none CN1CCC2=CC=C(NC(=O)C3=CC4=C(N3)C(C(=O)[O-])=CS4)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 29, 29, 29, 29, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 13, 1, 1, 1, 29] 29 rigid atoms, others: [34, 35, 36, 9, 11, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37]) total number of confs: 58 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517373 none CN1CCC2=CC=C(NC(=O)C3=CC4=C(N3)C(C(=O)[O-])=CS4)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 9, 29, 29, 29, 1] 29 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 37, 32, 22, 23, 27, 28, 29, 30, 31] set([33, 34, 35, 36, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26]) total number of confs: 52 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517373 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517373 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517373/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517373 Building REAL300004517374 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517374' /scratch/stefan/7774842/working/building/REAL300004517374 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517374 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517374/0 /scratch/stefan/7774842/working/building/REAL300004517374 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 410) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/410 `/scratch/stefan/7774842/working/3D/410' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)C3=CC4=C(C=C(C(=O)[O-])S4)N3)C=C21) `REAL300004517374.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517374 none CN1CCC2=CC=C(NC(=O)C3=CC4=C(C=C(C(=O)[O-])S4)N3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 14, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 20, 20, 20, 20, 11, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 11, 1, 1, 1, 20] 20 rigid atoms, others: [34, 35, 36, 9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37]) total number of confs: 39 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517374 none CN1CCC2=CC=C(NC(=O)C3=CC4=C(C=C(C(=O)[O-])S4)N3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'N.pl3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 14, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 9, 20, 20, 20, 1] 20 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 37, 32, 22, 23, 27, 28, 29, 30, 31] set([33, 34, 35, 36, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26]) total number of confs: 42 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517374 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517374 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517374/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517374 Building REAL300004517375 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517375' /scratch/stefan/7774842/working/building/REAL300004517375 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517375 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517375/0 /scratch/stefan/7774842/working/building/REAL300004517375 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 411) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/411 `/scratch/stefan/7774842/working/3D/411' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)C3=CC4=C(N3)C(C(=O)[O-])=CO4)C=C21) `REAL300004517375.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517375.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517375/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517375 none CN1CCC2=CC=C(NC(=O)C3=CC4=C(N3)C(C(=O)[O-])=CO4)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [31, 31, 31, 31, 31, 31, 31, 13, 13, 1, 13, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 13, 1, 1, 1, 31] 31 rigid atoms, others: [34, 35, 36, 9, 11, 12, 13, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37]) total number of confs: 60 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517375 none CN1CCC2=CC=C(NC(=O)C3=CC4=C(N3)C(C(=O)[O-])=CO4)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 9, 31, 31, 31, 1] 31 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 37, 32, 22, 23, 27, 28, 29, 30, 31] set([33, 34, 35, 36, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26]) total number of confs: 54 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517375 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517375 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517375/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517375 Building REAL300004517376 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517376' /scratch/stefan/7774842/working/building/REAL300004517376 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517376 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517376/0 /scratch/stefan/7774842/working/building/REAL300004517376 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 412) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/412 `/scratch/stefan/7774842/working/3D/412' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=CC=C1C(=O)NC1=CC=C2CCN(C)C2=C1) `REAL300004517376.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517376.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517376/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517376 none CC1=C(C(=O)[O-])C=CC=C1C(=O)NC1=CC=C2CCN(C)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 19, 19, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 9, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1] 19 rigid atoms, others: [32, 33, 34, 35, 39, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 23, 24, 25, 26, 27, 28, 29, 36, 37, 38]) total number of confs: 41 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517376 none CC1=C(C(=O)[O-])C=CC=C1C(=O)NC1=CC=C2CCN(C)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 8, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 7, 7, 7, 19, 19, 19, 19, 19, 19, 19, 19, 19, 2, 2, 2, 1, 1, 1, 7, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19] 19 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 9, 10, 26, 27, 28] set([4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 43 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517376 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517376 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517376/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517376 Building REAL300004517377 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517377' /scratch/stefan/7774842/working/building/REAL300004517377 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517377 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517377/0 /scratch/stefan/7774842/working/building/REAL300004517377 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 413) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/413 `/scratch/stefan/7774842/working/3D/413' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)C=CC3=CC=C(C(=O)[O-])N=C3)C=C21) `REAL300004517377.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517377.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517377/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517377 none CN1CCC2=CC=C(NC(=O)C=CC3=CC=C(C(=O)[O-])N=C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [44, 44, 44, 44, 44, 44, 44, 22, 22, 5, 22, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 22, 5, 5, 1, 1, 1, 44] 44 rigid atoms, others: [36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39]) total number of confs: 88 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517377 none CN1CCC2=CC=C(NC(=O)C=CC3=CC=C(C(=O)[O-])N=C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 28, 29, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 9, 29, 29, 44, 44, 44, 1] 44 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 39, 32, 22, 23, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 33, 34, 35, 36, 37, 38]) total number of confs: 112 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517377 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517377 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517377/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517377 Building REAL300004517378 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517378' /scratch/stefan/7774842/working/building/REAL300004517378 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517378 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517378/0 /scratch/stefan/7774842/working/building/REAL300004517378 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 414) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/414 `/scratch/stefan/7774842/working/3D/414' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)C3=CC(C(=O)[O-])=CS3)C=C21) `REAL300004517378.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517378.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517378/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517378 none CN1CCC2=CC=C(NC(=O)C3=CC(C(=O)[O-])=CS3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 11, 11, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 23, 23, 23, 13, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 13, 1, 1, 23] 23 rigid atoms, others: [32, 9, 11, 12, 13, 14, 15, 16, 17, 18, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33]) total number of confs: 43 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517378 none CN1CCC2=CC=C(NC(=O)C3=CC(C(=O)[O-])=CS3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 11, 11, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 23, 23, 23, 23, 23, 23, 23, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 9, 23, 23, 1] 23 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 33, 19, 20, 24, 25, 26, 27, 28, 29] set([32, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 30, 31]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517378 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517378 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517378/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517378 Building REAL300004517379 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517379' /scratch/stefan/7774842/working/building/REAL300004517379 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517379 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517379/0 /scratch/stefan/7774842/working/building/REAL300004517379 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 415) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/415 `/scratch/stefan/7774842/working/3D/415' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)[C@@H]3[C@H]4CC[C@H](O4)[C@@H]3C(=O)[O-])C=C21) `REAL300004517379.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517379.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517379/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517379 none CN1CCC2=CC=C(NC(=O)[C@@H]3[C@H]4CC[C@H](O4)[C@@H]3C(=O)[O-])C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 7, 5, 5, 5, 7, 12, 5, 7, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 14, 4, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 4, 1, 1, 1, 1, 14] 14 rigid atoms, others: [37, 38, 39, 40, 9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41]) total number of confs: 27 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517379 none CN1CCC2=CC=C(NC(=O)[C@@H]3[C@H]4CC[C@H](O4)[C@@H]3C(=O)[O-])C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 7, 5, 5, 5, 7, 12, 5, 7, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 7, 14, 14, 14, 14, 1] 14 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 41, 7, 34, 35, 25, 26, 5, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 36, 37, 38, 39, 40]) total number of confs: 47 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517379 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517379 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517379/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517379 Building REAL300004517380 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517380' /scratch/stefan/7774842/working/building/REAL300004517380 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517380 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517380/0 /scratch/stefan/7774842/working/building/REAL300004517380 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 416) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/416 `/scratch/stefan/7774842/working/3D/416' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)C3=CC=CC4=C(C(=O)[O-])C=CC=C34)C=C21) `REAL300004517380.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517380.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517380/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517380 none CN1CCC2=CC=C(NC(=O)C3=CC=CC4=C(C(=O)[O-])C=CC=C34)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 8, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 8, 1, 1, 1, 1, 1, 1, 28] 28 rigid atoms, others: [36, 37, 38, 39, 40, 9, 41, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 42]) total number of confs: 49 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517380 none CN1CCC2=CC=C(NC(=O)C3=CC=CC4=C(C(=O)[O-])C=CC=C34)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 9, 28, 28, 28, 28, 28, 28, 1] 28 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 42, 7, 34, 24, 25, 33, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 50 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517380 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517380 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517380/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517380 Building REAL300004517381 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517381' /scratch/stefan/7774842/working/building/REAL300004517381 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517381 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517381/0 /scratch/stefan/7774842/working/building/REAL300004517381 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 417) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/417 `/scratch/stefan/7774842/working/3D/417' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@]1(C(=O)NC2=CC=C3CCN(C)C3=C2)C[C@H]1C(=O)[O-]) `REAL300004517381.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517381.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517381/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517381 none CC(C)[C@]1(C(=O)NC2=CC=C3CCN(C)C3=C2)C[C@H]1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 5, 5, 7, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [60, 34, 60, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 46, 46, 60, 60, 60, 60, 60, 60, 60, 11, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1, 34, 34] 60 rigid atoms, others: [32, 33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 40, 31] set([0, 1, 2, 3, 4, 5, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 37, 38, 39, 41, 42]) total number of confs: 275 number of broken/clashed sets: 23 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517381 none CC(C)[C@]1(C(=O)NC2=CC=C3CCN(C)C3=C2)C[C@H]1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 5, 5, 7, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [7, 1, 7, 1, 1, 5, 5, 5, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 1, 3, 3, 7, 7, 7, 7, 7, 7, 7, 5, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1] 60 rigid atoms, others: [1, 3, 4, 41, 42, 17, 18, 19, 20] set([0, 2, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 71 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517381 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517381 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517381/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517381 Building REAL300004517382 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517382' /scratch/stefan/7774842/working/building/REAL300004517382 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517382 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517382/0 /scratch/stefan/7774842/working/building/REAL300004517382 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 418) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/418 `/scratch/stefan/7774842/working/3D/418' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1CC(=O)NC1=CC=C2CCN(C)C2=C1) `REAL300004517382.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517382.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517382/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517382 none CC1=CC(C(=O)[O-])=CC=C1CC(=O)NC1=CC=C2CCN(C)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 11, 8, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [75, 75, 75, 63, 75, 75, 75, 75, 75, 53, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 75, 75, 75, 75, 75, 75, 53, 53, 10, 1, 1, 1, 1, 1, 1, 2, 2, 2, 1] 75 rigid atoms, others: [33, 34, 35, 36, 37, 38, 42, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 24, 25, 26, 27, 28, 29, 30, 31, 32, 39, 40, 41]) total number of confs: 276 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517382 none CC1=CC(C(=O)[O-])=CC=C1CC(=O)NC1=CC=C2CCN(C)C2=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 11, 8, 1, 1, 1, 1, 5, 5, 8, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 75 conformations in input total number of sets (complete confs): 75 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 6, 29, 29, 29, 75, 75, 75, 75, 75, 75, 75, 75, 75, 2, 2, 2, 1, 1, 1, 6, 6, 29, 75, 75, 75, 75, 75, 75, 75, 75, 75, 75] 75 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 27, 28, 29] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517382 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517382 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517382/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517382 Building REAL300004517383 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517383' /scratch/stefan/7774842/working/building/REAL300004517383 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517383 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517383/0 /scratch/stefan/7774842/working/building/REAL300004517383 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 419) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/419 `/scratch/stefan/7774842/working/3D/419' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)CC3=CC(C(=O)[O-])=CS3)C=C21) `REAL300004517383.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517383/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517383 none CN1CCC2=CC=C(NC(=O)CC3=CC(C(=O)[O-])=CS3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 1, 1, 1, 1, 11, 11, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [134, 134, 134, 134, 134, 134, 134, 54, 54, 9, 54, 1, 1, 1, 1, 1, 1, 1, 1, 1, 134, 134, 134, 134, 134, 134, 134, 134, 134, 134, 134, 54, 9, 9, 1, 1, 134] 134 rigid atoms, others: [34, 35, 11, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36]) total number of confs: 254 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517383 none CN1CCC2=CC=C(NC(=O)CC3=CC(C(=O)[O-])=CS3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 1, 1, 1, 1, 11, 11, 1, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 134 conformations in input total number of sets (complete confs): 134 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 67, 134, 134, 134, 134, 134, 134, 134, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 11, 67, 67, 134, 134, 1] 134 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 20, 21, 25, 26, 27, 28, 29, 30, 36] set([32, 33, 34, 35, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 23, 24, 31]) total number of confs: 335 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517383 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517383 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517383/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517383 Building REAL300004517384 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517384' /scratch/stefan/7774842/working/building/REAL300004517384 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517384 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517384/0 /scratch/stefan/7774842/working/building/REAL300004517384 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 420) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/420 `/scratch/stefan/7774842/working/3D/420' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)CC3=CC=C(C(=O)[O-])C(F)=C3)C=C21) `REAL300004517384.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517384.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517384/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517384 none CN1CCC2=CC=C(NC(=O)CC3=CC=C(C(=O)[O-])C(F)=C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [121, 121, 121, 121, 121, 121, 121, 17, 17, 6, 17, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 121, 121, 121, 121, 121, 121, 121, 121, 121, 121, 121, 17, 6, 6, 1, 1, 1, 121] 121 rigid atoms, others: [36, 37, 38, 11, 12, 13, 14, 15, 16, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39]) total number of confs: 179 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517384 none CN1CCC2=CC=C(NC(=O)CC3=CC=C(C(=O)[O-])C(F)=C3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 121 conformations in input total number of sets (complete confs): 121 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 35, 121, 121, 121, 121, 121, 121, 121, 121, 121, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 11, 35, 35, 121, 121, 121, 1] 121 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 39, 32, 22, 23, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 33, 34, 35, 36, 37, 38]) total number of confs: 251 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517384 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517384 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517384/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517384 Building REAL300004517385 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517385' /scratch/stefan/7774842/working/building/REAL300004517385 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517385 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517385/0 /scratch/stefan/7774842/working/building/REAL300004517385 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 421) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/421 `/scratch/stefan/7774842/working/3D/421' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)C3=C4CCCCC4=C(C(=O)[O-])S3)C=C21) `REAL300004517385.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517385.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517385/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517385 none CN1CCC2=CC=C(NC(=O)C3=C4CCCCC4=C(C(=O)[O-])S3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 5, 5, 5, 5, 1, 1, 1, 11, 11, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 34, 34, 34, 34, 10, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 10, 1, 1, 1, 1, 1, 1, 1, 1, 34] 34 rigid atoms, others: [35, 36, 37, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 43]) total number of confs: 56 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517385 none CN1CCC2=CC=C(NC(=O)C3=C4CCCCC4=C(C(=O)[O-])S3)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 1, 1, 5, 5, 5, 5, 1, 1, 1, 11, 11, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 9, 34, 34, 34, 34, 34, 34, 34, 34, 1] 34 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 8, 7, 43, 23, 24, 33, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 56 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517385 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517385 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517385/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517385 Building REAL300004517386 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517386' /scratch/stefan/7774842/working/building/REAL300004517386 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517386 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517386/0 /scratch/stefan/7774842/working/building/REAL300004517386 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 422) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/422 `/scratch/stefan/7774842/working/3D/422' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCC2=CC=C(NC(=O)C34CCC(C(=O)[O-])(CC3)CC4)C=C21) `REAL300004517386.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517386.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517386/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517386 none CN1CCC2=CC=C(NC(=O)C34CCC(C(=O)[O-])(CC3)CC4)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 4, 4, 1, 4, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11] 11 rigid atoms, others: [9, 11, 12, 13, 14, 15, 18, 19, 20, 21, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 46]) total number of confs: 25 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517386 none CN1CCC2=CC=C(NC(=O)C34CCC(C(=O)[O-])(CC3)CC4)C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 11, 11, 7, 7, 11, 11, 11, 11, 11, 11, 1, 1, 2, 2, 2, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1] 11 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 46, 32, 22, 23, 27, 28, 29, 30, 31] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517386 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517386 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517386/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517386 Building REAL300004517387 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517387' /scratch/stefan/7774842/working/building/REAL300004517387 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517387 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517387/0 /scratch/stefan/7774842/working/building/REAL300004517387 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 423) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/423 `/scratch/stefan/7774842/working/3D/423' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1=CC=CC=N1)C(=O)C1=CC=CC(OCC(=O)[O-])=C1) `REAL300004517387.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517387 none CN(CC1=CC=CC=N1)C(=O)C1=CC=CC(OCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 9, 19, 49, 63, 63, 63, 63, 63, 1, 9, 1, 1, 1, 1, 1, 1, 6, 17, 26, 26, 1, 19, 19, 19, 49, 49, 63, 63, 63, 63, 1, 1, 1, 17, 17, 1] 201 rigid atoms, others: [32, 33, 36, 9, 11, 12, 13, 14, 15, 16, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35]) total number of confs: 284 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517387 none CN(CC1=CC=CC=N1)C(=O)C1=CC=CC(OCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 7, 1, 1, 1, 1, 1, 1, 1, 15, 42, 42, 63, 63, 63, 63, 63, 139, 201, 201, 201, 63, 15, 15, 15, 7, 7, 1, 1, 1, 1, 63, 63, 63, 201, 201, 63] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 27, 28, 29, 30] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36]) total number of confs: 614 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517387 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517387 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517387/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517387 Building REAL300004517388 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517388' /scratch/stefan/7774842/working/building/REAL300004517388 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517388 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517388/0 /scratch/stefan/7774842/working/building/REAL300004517388 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 424) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/424 `/scratch/stefan/7774842/working/3D/424' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1=CC=CC=N1)C(=O)C1CCCN1S(=O)(=O)C1=CC=C(C(=O)[O-])O1) `REAL300004517388.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517388.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517388/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517388 none CN(CC1=CC=CC=N1)C(=O)C1CCCN1S(=O)(=O)C1=CC=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 5, 14, 45, 62, 62, 62, 62, 62, 1, 5, 1, 1, 1, 1, 1, 1, 6, 6, 6, 35, 35, 35, 35, 35, 35, 35, 14, 14, 14, 45, 45, 62, 62, 62, 62, 1, 1, 1, 1, 1, 1, 1, 35, 35] 201 rigid atoms, others: [36, 37, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 43, 44]) total number of confs: 241 number of broken/clashed sets: 125 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517388 none CN(CC1=CC=CC=N1)C(=O)C1CCCN1S(=O)(=O)C1=CC=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 9, 1, 1, 1, 1, 1, 1, 1, 23, 46, 46, 62, 62, 62, 62, 62, 137, 137, 137, 201, 201, 201, 201, 201, 201, 201, 23, 23, 23, 9, 9, 1, 1, 1, 1, 62, 62, 62, 62, 62, 62, 62, 201, 201] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 642 number of broken/clashed sets: 125 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517388 none CN(CC1=CC=CC=N1)C(=O)C1CCCN1S(=O)(=O)C1=CC=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [139, 55, 139, 195, 201, 201, 201, 201, 201, 35, 55, 35, 35, 35, 35, 9, 1, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 139, 139, 139, 195, 195, 201, 201, 201, 201, 35, 35, 35, 35, 35, 35, 35, 1, 1] 201 rigid atoms, others: [43, 44, 16, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 695 number of broken/clashed sets: 125 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517388 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517388 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517388/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517388 Building REAL300004517389 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517389' /scratch/stefan/7774842/working/building/REAL300004517389 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517389 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517389/0 /scratch/stefan/7774842/working/building/REAL300004517389 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 425) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/425 `/scratch/stefan/7774842/working/3D/425' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1=CC=CC=N1)C(=O)C1=CC=CC=C1SCC1=C(C(=O)[O-])C=CO1) `REAL300004517389.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517389 none CN(CC1=CC=CC=N1)C(=O)C1=CC=CC=C1SCC1=C(C(=O)[O-])C=CO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 14, 5, 1, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 7, 9, 25, 32, 32, 32, 32, 32, 1, 7, 1, 1, 1, 1, 1, 1, 1, 7, 29, 68, 68, 68, 68, 68, 68, 68, 9, 9, 9, 25, 25, 32, 32, 32, 32, 1, 1, 1, 1, 29, 29, 68, 68] 201 rigid atoms, others: [36, 37, 38, 39, 9, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43]) total number of confs: 265 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517389 none CN(CC1=CC=CC=N1)C(=O)C1=CC=CC=C1SCC1=C(C(=O)[O-])C=CO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 14, 5, 1, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 7, 1, 1, 1, 1, 1, 1, 1, 11, 23, 23, 32, 32, 32, 32, 32, 32, 74, 158, 201, 201, 201, 201, 201, 201, 201, 11, 11, 11, 7, 7, 1, 1, 1, 1, 32, 32, 32, 32, 158, 158, 201, 201] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 35] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 619 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517389 none CN(CC1=CC=CC=N1)C(=O)C1=CC=CC=C1SCC1=C(C(=O)[O-])C=CO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 14, 5, 1, 1, 1, 11, 11, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [114, 112, 114, 201, 201, 201, 201, 201, 201, 66, 112, 68, 68, 68, 68, 68, 24, 6, 1, 1, 1, 1, 2, 2, 1, 1, 1, 114, 114, 114, 201, 201, 201, 201, 201, 201, 68, 68, 68, 68, 6, 6, 1, 1] 201 rigid atoms, others: [42, 43, 18, 19, 20, 21, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 697 number of broken/clashed sets: 10 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517389 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517389 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517389/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517389 Building REAL300004517390 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517390' /scratch/stefan/7774842/working/building/REAL300004517390 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517390 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517390/0 /scratch/stefan/7774842/working/building/REAL300004517390 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 426) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/426 `/scratch/stefan/7774842/working/3D/426' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(SC1=CC=CC=C1C(=O)N(C)CC1=CC=CC=N1)C(=O)[O-]) `REAL300004517390.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517390/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517390 none CC(SC1=CC=CC=C1C(=O)N(C)CC1=CC=CC=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [8, 7, 7, 7, 7, 7, 7, 7, 6, 5, 6, 3, 5, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 7, 7, 7, 7, 5, 5, 5, 3, 3, 1, 1, 1, 1] 8 rigid atoms, others: [36, 37, 38, 39, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 30 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517390 none CC(SC1=CC=CC=C1C(=O)N(C)CC1=CC=CC=N1)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 14, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 8, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 8 conformations in input total number of sets (complete confs): 8 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 7, 7, 7, 7, 7, 7, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 4, 4, 4, 7, 7, 7, 7, 7, 7] 8 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 9, 27, 28, 29, 30] set([0, 1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 33 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517390 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517390 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517390/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517390 Building REAL300004517391 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517391' /scratch/stefan/7774842/working/building/REAL300004517391 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517391 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517391/0 /scratch/stefan/7774842/working/building/REAL300004517391 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 427) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/427 `/scratch/stefan/7774842/working/3D/427' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C(=O)N(C)CC2=CC=CC=N2)=CC=C1OCC(=O)[O-]) `REAL300004517391.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517391/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517391 none CCOC1=CC(C(=O)N(C)CC2=CC=CC=N2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 56, 23, 23, 23, 11, 9, 11, 7, 9, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 93, 178, 187, 187, 71, 71, 71, 71, 71, 23, 9, 9, 9, 7, 7, 1, 1, 1, 1, 23, 23, 178, 178] 201 rigid atoms, others: [36, 37, 38, 39, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43]) total number of confs: 722 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517391 none CCOC1=CC(C(=O)N(C)CC2=CC=CC=N2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 7, 1, 1, 1, 1, 1, 7, 7, 11, 11, 17, 23, 23, 23, 23, 23, 1, 1, 1, 1, 9, 35, 58, 58, 21, 21, 21, 21, 21, 1, 11, 11, 11, 17, 17, 23, 23, 23, 23, 1, 1, 35, 35] 201 rigid atoms, others: [2, 3, 4, 5, 6, 40, 41, 17, 18, 19, 20, 30] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 42, 43]) total number of confs: 319 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517391 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517391 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517391/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517391 Building REAL300004517392 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517392' /scratch/stefan/7774842/working/building/REAL300004517392 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517392 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517392/0 /scratch/stefan/7774842/working/building/REAL300004517392 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 428) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/428 `/scratch/stefan/7774842/working/3D/428' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1=CC=CC=N1)C(=O)CNS(=O)(=O)C1=CC=C(C(=O)[O-])C=C1) `REAL300004517392.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517392/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517392 none CN(CC1=CC=CC=N1)C(=O)CNS(=O)(=O)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 51, 73, 163, 201, 201, 201, 201, 201, 25, 51, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 73, 73, 73, 163, 163, 201, 201, 201, 201, 25, 25, 5, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 725 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517392 none CN(CC1=CC=CC=N1)C(=O)CNS(=O)(=O)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 9, 1, 1, 1, 1, 1, 1, 1, 33, 65, 65, 91, 153, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 33, 33, 33, 9, 9, 1, 1, 1, 1, 91, 91, 153, 201, 201, 201, 201] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 784 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517392 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517392 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517392/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517392 Building REAL300004517393 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517393' /scratch/stefan/7774842/working/building/REAL300004517393 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517393 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517393/0 /scratch/stefan/7774842/working/building/REAL300004517393 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 429) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/429 `/scratch/stefan/7774842/working/3D/429' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1=CC=CC=N1)C(=O)C1=CC(C(=O)[O-])=CC([N+](=O)[O-])=C1) `REAL300004517393.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517393.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517393/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517393 none CN(CC1=CC=CC=N1)C(=O)C1=CC(C(=O)[O-])=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 11, 35, 134, 201, 201, 201, 201, 201, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 134, 134, 201, 201, 201, 201, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 601 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517393 none CN(CC1=CC=CC=N1)C(=O)C1=CC(C(=O)[O-])=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 9, 1, 1, 1, 1, 1, 1, 1, 35, 103, 103, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 35, 35, 35, 9, 9, 1, 1, 1, 1, 201, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 28, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34]) total number of confs: 444 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517393 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517393 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517393/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517393 Building REAL300004517394 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517394' /scratch/stefan/7774842/working/building/REAL300004517394 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517394 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517394/0 /scratch/stefan/7774842/working/building/REAL300004517394 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 430) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/430 `/scratch/stefan/7774842/working/3D/430' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NN(C2=CC=C(C(=O)N(C)CC3=CC=CC=N3)C=C2)C(C)=C1CCC(=O)[O-]) `REAL300004517394.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517394/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517394 none CC1=NN(C2=CC=C(C(=O)N(C)CC3=CC=CC=N3)C=C2)C(C)=C1CCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 5, 1, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [4, 4, 4, 1, 1, 1, 1, 1, 1, 7, 7, 21, 21, 60, 80, 80, 80, 80, 80, 1, 1, 4, 4, 4, 4, 7, 7, 11, 11, 4, 4, 4, 1, 1, 21, 21, 21, 60, 60, 80, 80, 80, 80, 1, 1, 4, 4, 4, 7, 7, 7, 7] 201 rigid atoms, others: [32, 33, 3, 4, 5, 6, 7, 8, 43, 44, 19, 20] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 294 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517394 none CC1=NN(C2=CC=C(C(=O)N(C)CC3=CC=CC=N3)C=C2)C(C)=C1CCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 5, 1, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 4, 4, 1, 3, 14, 14, 39, 40, 110, 144, 144, 144, 144, 144, 4, 4, 1, 1, 1, 1, 2, 2, 6, 6, 2, 2, 2, 4, 4, 40, 39, 39, 110, 110, 144, 144, 144, 144, 4, 4, 2, 2, 2, 2, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 21, 22, 23, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 498 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517394 none CC1=NN(C2=CC=C(C(=O)N(C)CC3=CC=CC=N3)C=C2)C(C)=C1CCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 5, 1, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [144, 144, 144, 80, 54, 80, 80, 27, 13, 27, 8, 13, 1, 1, 1, 1, 1, 1, 1, 80, 80, 144, 144, 144, 144, 201, 201, 201, 201, 144, 144, 144, 80, 80, 13, 13, 13, 8, 8, 1, 1, 1, 1, 80, 80, 144, 144, 144, 201, 201, 201, 201] 201 rigid atoms, others: [39, 40, 41, 42, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 744 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517394 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517394 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517394/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517394 Building REAL300004517395 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517395' /scratch/stefan/7774842/working/building/REAL300004517395 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517395 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517395/0 /scratch/stefan/7774842/working/building/REAL300004517395 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 431) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/431 `/scratch/stefan/7774842/working/3D/431' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1=CC=CC=N1)C(=O)C1=CC(C(=O)[O-])=CC([N+](=O)[O-])=C1) `REAL300004517395.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517395/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517395 none CN(CC1=CC=CC=N1)C(=O)C1=CC(C(=O)[O-])=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 11, 35, 134, 201, 201, 201, 201, 201, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 134, 134, 201, 201, 201, 201, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 601 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517395 none CN(CC1=CC=CC=N1)C(=O)C1=CC(C(=O)[O-])=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 9, 1, 1, 1, 1, 1, 1, 1, 35, 103, 103, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 35, 35, 35, 9, 9, 1, 1, 1, 1, 201, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 28, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34]) total number of confs: 444 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517395 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517395 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517395/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517395 Building REAL300004517396 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517396' /scratch/stefan/7774842/working/building/REAL300004517396 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517396 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517396/0 /scratch/stefan/7774842/working/building/REAL300004517396 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 432) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/432 `/scratch/stefan/7774842/working/3D/432' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=NN1C1=CC=C(C(=O)N(C)CC2=CC=CC=N2)C=C1) `REAL300004517396.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517396.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517396/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517396 none CC1=C(C(=O)[O-])C=NN1C1=CC=C(C(=O)N(C)CC2=CC=CC=N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 8, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 7, 7, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 25, 25, 59, 114, 114, 114, 114, 114, 1, 1, 5, 5, 5, 5, 1, 1, 25, 25, 25, 59, 59, 114, 114, 114, 114, 1, 1] 201 rigid atoms, others: [8, 9, 10, 11, 12, 13, 41, 24, 25, 42, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 317 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517396 none CC1=C(C(=O)[O-])C=NN1C1=CC=C(C(=O)N(C)CC2=CC=CC=N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 8, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 5, 5, 2, 3, 15, 15, 49, 49, 109, 201, 201, 201, 201, 201, 5, 5, 2, 2, 2, 1, 5, 5, 49, 49, 49, 109, 109, 201, 201, 201, 201, 5, 5] 201 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 9, 29] set([4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 558 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517396 none CC1=C(C(=O)[O-])C=NN1C1=CC=C(C(=O)N(C)CC2=CC=CC=N2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 8, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 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, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 201, 201, 201, 201, 100, 94, 114, 114, 49, 19, 49, 8, 19, 1, 1, 1, 1, 1, 1, 1, 114, 114, 201, 201, 201, 201, 114, 114, 19, 19, 19, 8, 8, 1, 1, 1, 1, 114, 114] 201 rigid atoms, others: [37, 38, 39, 40, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42]) total number of confs: 506 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517396 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517396 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517396/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517396 Building REAL300004517397 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517397' /scratch/stefan/7774842/working/building/REAL300004517397 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517397 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517397/0 /scratch/stefan/7774842/working/building/REAL300004517397 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 433) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/433 `/scratch/stefan/7774842/working/3D/433' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1=CC=CC=N1)C(=O)C1=CC(C(=O)[O-])=NN1C1=CC=CC=C1) `REAL300004517397.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517397.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517397/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517397 none CN(CC1=CC=CC=N1)C(=O)C1=CC(C(=O)[O-])=NN1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 11, 11, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 9, 31, 129, 185, 185, 185, 185, 185, 1, 9, 1, 1, 1, 1, 2, 2, 1, 1, 1, 5, 5, 1, 5, 5, 31, 31, 31, 129, 129, 185, 185, 185, 185, 1, 5, 5, 1, 5, 5] 201 rigid atoms, others: [34, 9, 11, 12, 13, 14, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39]) total number of confs: 571 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517397 none CN(CC1=CC=CC=N1)C(=O)C1=CC(C(=O)[O-])=NN1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 11, 11, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 9, 1, 1, 1, 1, 1, 1, 1, 30, 97, 97, 185, 185, 185, 185, 185, 185, 185, 185, 201, 201, 201, 201, 201, 30, 30, 30, 9, 9, 1, 1, 1, 1, 185, 201, 201, 201, 201, 201] 201 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39]) total number of confs: 444 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517397 none CN(CC1=CC=CC=N1)C(=O)C1=CC(C(=O)[O-])=NN1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 11, 11, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 19, 53, 156, 201, 201, 201, 201, 201, 5, 19, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 53, 53, 53, 156, 156, 201, 201, 201, 201, 5, 1, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 39, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 637 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517397 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517397 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517397/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517397 Building REAL300004517398 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517398' /scratch/stefan/7774842/working/building/REAL300004517398 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517398 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517398/0 /scratch/stefan/7774842/working/building/REAL300004517398 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 434) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/434 `/scratch/stefan/7774842/working/3D/434' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)N(C)CC2=CC=CC=N2)=CC(C)=C1OCC(=O)[O-]) `REAL300004517398.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517398.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517398/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517398 none CC1=CC(C(=O)N(C)CC2=CC=CC=N2)=CC(C)=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 8, 1, 1, 5, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [111, 111, 111, 45, 15, 45, 8, 15, 1, 1, 1, 1, 1, 1, 1, 111, 111, 111, 45, 45, 117, 201, 201, 201, 111, 111, 111, 111, 15, 15, 15, 8, 8, 1, 1, 1, 1, 111, 111, 111, 111, 201, 201] 201 rigid atoms, others: [33, 34, 35, 36, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42]) total number of confs: 938 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517398 none CC1=CC(C(=O)N(C)CC2=CC=CC=N2)=CC(C)=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 8, 1, 1, 5, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 7, 7, 26, 26, 65, 111, 111, 111, 111, 111, 1, 1, 1, 1, 1, 2, 14, 22, 22, 2, 2, 2, 1, 26, 26, 26, 65, 65, 111, 111, 111, 111, 1, 2, 2, 2, 14, 14] 201 rigid atoms, others: [0, 1, 2, 3, 4, 37, 15, 16, 17, 18, 19, 27] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40, 41, 42]) total number of confs: 389 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517398 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517398 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517398/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517398 Building REAL300004517399 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517399' /scratch/stefan/7774842/working/building/REAL300004517399 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517399 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517399/0 /scratch/stefan/7774842/working/building/REAL300004517399 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 435) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/435 `/scratch/stefan/7774842/working/3D/435' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1=CC=CC=N1)C(=O)C1=CC(Br)=CC(C(=O)[O-])=C1) `REAL300004517399.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517399.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517399/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517399 none CN(CC1=CC=CC=N1)C(=O)C1=CC(Br)=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 17, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 11, 35, 133, 201, 201, 201, 201, 201, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 133, 133, 201, 201, 201, 201, 1, 1, 1] 201 rigid atoms, others: [32, 9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 606 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517399 none CN(CC1=CC=CC=N1)C(=O)C1=CC(Br)=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 17, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 9, 1, 1, 1, 1, 1, 1, 1, 37, 110, 110, 201, 201, 201, 201, 201, 201, 201, 201, 201, 37, 37, 37, 9, 9, 1, 1, 1, 1, 201, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 26, 27, 28, 29] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32]) total number of confs: 456 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517399 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517399 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517399/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517399 Building REAL300004517400 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517400' /scratch/stefan/7774842/working/building/REAL300004517400 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517400 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517400/0 /scratch/stefan/7774842/working/building/REAL300004517400 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 436) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/436 `/scratch/stefan/7774842/working/3D/436' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1=CC=CC=N1)C(=O)C1=CC=CC=C1C1=CC=CC=C1C(=O)[O-]) `REAL300004517400.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517400 none CN(CC1=CC=CC=N1)C(=O)C1=CC=CC=C1C1=CC=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 5, 7, 23, 23, 23, 23, 23, 23, 1, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 2, 3, 3, 3, 5, 5, 7, 7, 7, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 3, 3, 3, 3] 23 rigid atoms, others: [35, 36, 37, 38, 9, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42]) total number of confs: 101 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517400 none CN(CC1=CC=CC=N1)C(=O)C1=CC=CC=C1C1=CC=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 1, 1, 1, 1, 1, 1, 1, 10, 14, 14, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 10, 10, 10, 6, 6, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23] 23 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 34, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 60 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517400 none CN(CC1=CC=CC=N1)C(=O)C1=CC=CC=C1C1=CC=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 5, 7, 23, 23, 23, 23, 23, 23, 3, 5, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 7, 7, 23, 23, 23, 23, 23, 23, 3, 3, 3, 3, 1, 1, 1, 1] 23 rigid atoms, others: [39, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 92 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517400 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517400 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517400/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517400 Building REAL300004517401 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517401' /scratch/stefan/7774842/working/building/REAL300004517401 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517401 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517401/0 /scratch/stefan/7774842/working/building/REAL300004517401 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 437) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/437 `/scratch/stefan/7774842/working/3D/437' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1=CC=CC=N1)C(=O)C12CCC(C(=O)[O-])(CC1)CC2) `REAL300004517401.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517401.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517401/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517401 none CN(CC1=CC=CC=N1)C(=O)C12CCC(C(=O)[O-])(CC1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 8, 9, 15, 15, 15, 15, 15, 1, 4, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 8, 8, 8, 9, 9, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 15 rigid atoms, others: [9, 11, 12, 13, 14, 15, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 47 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517401 none CN(CC1=CC=CC=N1)C(=O)C12CCC(C(=O)[O-])(CC1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [13, 7, 1, 1, 1, 1, 1, 1, 1, 13, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 13, 13, 13, 7, 7, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 15 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 27, 28, 29, 30] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 50 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517401 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517401 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517401/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517401 Building REAL300004517402 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517402' /scratch/stefan/7774842/working/building/REAL300004517402 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517402 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517402/0 /scratch/stefan/7774842/working/building/REAL300004517402 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 438) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/438 `/scratch/stefan/7774842/working/3D/438' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1=CC=CC=N1)C(=O)C1=CC=NC2=C(C(=O)[O-])C=NN21) `REAL300004517402.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517402.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517402/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517402 none CN(CC1=CC=CC=N1)C(=O)C1=CC=NC2=C(C(=O)[O-])C=NN21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 9, 32, 114, 201, 201, 201, 201, 201, 1, 9, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 32, 32, 32, 114, 114, 201, 201, 201, 201, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 9, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 549 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517402 none CN(CC1=CC=CC=N1)C(=O)C1=CC=NC2=C(C(=O)[O-])C=NN21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [36, 9, 1, 1, 1, 1, 1, 1, 1, 36, 114, 114, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 36, 36, 36, 9, 9, 1, 1, 1, 1, 201, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 28, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34]) total number of confs: 453 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517402 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517402 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517402/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517402 Building REAL300004517403 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517403' /scratch/stefan/7774842/working/building/REAL300004517403 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517403 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517403/0 /scratch/stefan/7774842/working/building/REAL300004517403 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 439) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/439 `/scratch/stefan/7774842/working/3D/439' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1=CC=CC=N1)C(=O)C1=C(CC(=O)[O-])C2=CC=CC=C2N1) `REAL300004517403.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517403/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517403 none CN(CC1=CC=CC=N1)C(=O)C1=C(CC(=O)[O-])C2=CC=CC=C2N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [23, 9, 23, 66, 83, 83, 83, 83, 83, 1, 9, 1, 1, 1, 2, 7, 7, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 66, 66, 83, 83, 83, 83, 2, 2, 1, 1, 1, 1, 1] 85 rigid atoms, others: [35, 36, 37, 38, 39, 9, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 296 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517403 none CN(CC1=CC=CC=N1)C(=O)C1=C(CC(=O)[O-])C2=CC=CC=C2N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [25, 8, 1, 1, 1, 1, 1, 1, 1, 25, 61, 61, 83, 83, 85, 85, 85, 83, 83, 83, 83, 83, 83, 83, 25, 25, 25, 8, 8, 1, 1, 1, 1, 85, 85, 83, 83, 83, 83, 83] 85 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517403 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517403 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517403/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517403 Building REAL300004517404 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517404' /scratch/stefan/7774842/working/building/REAL300004517404 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517404 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517404/0 /scratch/stefan/7774842/working/building/REAL300004517404 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 440) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/440 `/scratch/stefan/7774842/working/3D/440' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1=CC=CC=N1)C(=O)CC1CCCC2=CC=C(C(=O)[O-])C=C21) `REAL300004517404.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517404.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517404/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517404 none CN(CC1=CC=CC=N1)C(=O)CC1CCCC2=CC=C(C(=O)[O-])C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [16, 7, 16, 27, 27, 27, 27, 27, 27, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 16, 16, 16, 27, 27, 27, 27, 27, 27, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 27 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 23, 24, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 111 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517404 none CN(CC1=CC=CC=N1)C(=O)CC1CCCC2=CC=C(C(=O)[O-])C=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [14, 6, 1, 1, 1, 1, 1, 1, 1, 14, 21, 21, 25, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 14, 14, 14, 6, 6, 1, 1, 1, 1, 25, 25, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27] 27 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 99 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517404 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517404 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517404/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517404 Building REAL300004517405 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517405' /scratch/stefan/7774842/working/building/REAL300004517405 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517405 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517405/0 /scratch/stefan/7774842/working/building/REAL300004517405 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 441) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/441 `/scratch/stefan/7774842/working/3D/441' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1=CC=CC=N1)C(=O)C1=CC=C(OCC(=O)[O-])C=C1) `REAL300004517405.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517405/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517405 none CN(CC1=CC=CC=N1)C(=O)C1=CC=C(OCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 6, 15, 33, 42, 42, 42, 42, 42, 1, 6, 1, 1, 1, 1, 1, 6, 18, 31, 31, 1, 1, 15, 15, 15, 33, 33, 42, 42, 42, 42, 1, 1, 18, 18, 1, 1] 201 rigid atoms, others: [32, 35, 36, 9, 11, 12, 13, 14, 15, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34]) total number of confs: 225 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517405 none CN(CC1=CC=CC=N1)C(=O)C1=CC=C(OCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [11, 7, 1, 1, 1, 1, 1, 1, 1, 11, 38, 38, 42, 42, 38, 39, 113, 201, 201, 201, 42, 42, 11, 11, 11, 7, 7, 1, 1, 1, 1, 42, 42, 201, 201, 42, 42] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 27, 28, 29, 30] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36]) total number of confs: 676 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517405 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517405 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517405/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517405 Building REAL300004517406 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517406' /scratch/stefan/7774842/working/building/REAL300004517406 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517406 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517406/0 /scratch/stefan/7774842/working/building/REAL300004517406 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 442) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/442 `/scratch/stefan/7774842/working/3D/442' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1=CC=CC=N1)C(=O)C1CC(C(=O)[O-])=NN1C1=CC=CC=C1) `REAL300004517406.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517406.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517406/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517406 none CN(CC1=CC=CC=N1)C(=O)C1CC(C(=O)[O-])=NN1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 1, 1, 11, 11, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [19, 5, 19, 49, 70, 70, 70, 70, 70, 1, 5, 1, 1, 1, 1, 7, 7, 1, 1, 1, 5, 5, 2, 5, 5, 19, 19, 19, 49, 49, 70, 70, 70, 70, 1, 1, 1, 5, 5, 5, 5, 5] 71 rigid atoms, others: [34, 35, 36, 9, 11, 12, 13, 14, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41]) total number of confs: 247 number of broken/clashed sets: 21 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517406 none CN(CC1=CC=CC=N1)C(=O)C1CC(C(=O)[O-])=NN1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 1, 1, 11, 11, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [25, 8, 1, 1, 1, 1, 1, 1, 1, 25, 50, 50, 70, 70, 70, 71, 71, 70, 70, 70, 71, 71, 71, 71, 71, 25, 25, 25, 8, 8, 1, 1, 1, 1, 70, 70, 70, 71, 71, 71, 71, 71] 71 rigid atoms, others: [32, 33, 2, 3, 4, 5, 6, 7, 8, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 225 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517406 none CN(CC1=CC=CC=N1)C(=O)C1CC(C(=O)[O-])=NN1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 1, 1, 11, 11, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [29, 12, 29, 59, 71, 71, 71, 71, 71, 5, 12, 5, 5, 5, 5, 14, 14, 5, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 59, 59, 71, 71, 71, 71, 5, 5, 5, 1, 1, 1, 1, 1] 71 rigid atoms, others: [37, 38, 39, 40, 41, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 266 number of broken/clashed sets: 21 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517406 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517406 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517406/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517406 Building REAL300004517407 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517407' /scratch/stefan/7774842/working/building/REAL300004517407 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517407 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517407/0 /scratch/stefan/7774842/working/building/REAL300004517407 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 443) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/443 `/scratch/stefan/7774842/working/3D/443' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1=CC=CC=N1)C(=O)COCC1=C(C(=O)[O-])N=CO1) `REAL300004517407.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517407/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517407 none CN(CC1=CC=CC=N1)C(=O)COCC1=C(C(=O)[O-])N=CO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 1, 11, 11, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [24, 16, 24, 47, 53, 53, 53, 53, 53, 12, 16, 8, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 47, 47, 53, 53, 53, 53, 12, 12, 5, 5, 1] 53 rigid atoms, others: [35, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 199 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517407 none CN(CC1=CC=CC=N1)C(=O)COCC1=C(C(=O)[O-])N=CO1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 1, 11, 11, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [22, 7, 1, 1, 1, 1, 1, 1, 1, 22, 40, 40, 44, 47, 53, 53, 53, 53, 53, 53, 53, 53, 22, 22, 22, 7, 7, 1, 1, 1, 1, 44, 44, 53, 53, 53] 53 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 27, 28, 29, 30] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517407 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517407 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517407/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517407 Building REAL300004517408 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517408' /scratch/stefan/7774842/working/building/REAL300004517408 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517408 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517408/0 /scratch/stefan/7774842/working/building/REAL300004517408 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 444) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/444 `/scratch/stefan/7774842/working/3D/444' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1=CC=CC=N1)C(=O)CCCN1C=CC(C(=O)[O-])=N1) `REAL300004517408.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517408/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517408 none CN(CC1=CC=CC=N1)C(=O)CCCN1C=CC(C(=O)[O-])=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 1, 11, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [97, 57, 97, 185, 201, 201, 201, 201, 201, 27, 57, 15, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 97, 97, 97, 185, 185, 201, 201, 201, 201, 27, 27, 15, 15, 7, 7, 1, 1] 201 rigid atoms, others: [37, 38, 13, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 800 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517408 none CN(CC1=CC=CC=N1)C(=O)CCCN1C=CC(C(=O)[O-])=N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 1, 11, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 8, 1, 1, 1, 1, 1, 1, 1, 27, 65, 65, 99, 121, 149, 201, 201, 201, 201, 201, 201, 201, 27, 27, 27, 8, 8, 1, 1, 1, 1, 99, 99, 121, 121, 149, 149, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 27, 28, 29, 30] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 725 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517408 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517408 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517408/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517408 Building REAL300004517409 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517409' /scratch/stefan/7774842/working/building/REAL300004517409 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517409 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517409/0 /scratch/stefan/7774842/working/building/REAL300004517409 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 445) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/445 `/scratch/stefan/7774842/working/3D/445' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1=CC=CC=N1)C(=O)[C@@H]1C2C=CC(CC2)[C@@H]1C(=O)[O-]) `REAL300004517409.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517409/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517409 none CN(CC1=CC=CC=N1)C(=O)[C@@H]1C2C=CC(CC2)[C@@H]1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 1, 1, 5, 5, 5, 5, 7, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 4, 10, 16, 16, 16, 16, 16, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 4, 4, 10, 10, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1] 16 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 32, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 49 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517409 none CN(CC1=CC=CC=N1)C(=O)[C@@H]1C2C=CC(CC2)[C@@H]1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 1, 1, 5, 5, 5, 5, 7, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [16, 8, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8, 8, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16] 16 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 51 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517409 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517409 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517409/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517409 Building REAL300004517410 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517410' /scratch/stefan/7774842/working/building/REAL300004517410 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517410 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517410/0 /scratch/stefan/7774842/working/building/REAL300004517410 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 446) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/446 `/scratch/stefan/7774842/working/3D/446' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1=CC=CC=N1)C(=O)C1(C(=O)[O-])CC1C1=CC=CC=C1) `REAL300004517410.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517410/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517410 none CN(CC1=CC=CC=N1)C(=O)C1(C(=O)[O-])CC1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 1, 11, 11, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [12, 5, 12, 43, 60, 60, 60, 60, 60, 1, 5, 1, 1, 3, 3, 1, 1, 1, 2, 2, 2, 2, 2, 12, 12, 12, 43, 43, 60, 60, 60, 60, 1, 1, 1, 2, 2, 2, 2, 2] 60 rigid atoms, others: [32, 33, 34, 9, 11, 12, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39]) total number of confs: 195 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517410 none CN(CC1=CC=CC=N1)C(=O)C1(C(=O)[O-])CC1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 1, 11, 11, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [28, 8, 1, 1, 1, 1, 1, 1, 1, 28, 55, 55, 60, 60, 60, 60, 60, 60, 60, 60, 60, 60, 60, 28, 28, 28, 8, 8, 1, 1, 1, 1, 60, 60, 60, 60, 60, 60, 60, 60] 60 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 28, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 177 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517410 none CN(CC1=CC=CC=N1)C(=O)C1(C(=O)[O-])CC1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 1, 11, 11, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [12, 5, 12, 43, 60, 60, 60, 60, 60, 2, 5, 2, 2, 3, 3, 2, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 43, 43, 60, 60, 60, 60, 2, 2, 2, 1, 1, 1, 1, 1] 60 rigid atoms, others: [35, 36, 37, 38, 39, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 193 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517410 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517410 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517410/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517410 Building REAL300004517411 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517411' /scratch/stefan/7774842/working/building/REAL300004517411 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517411 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517411/0 /scratch/stefan/7774842/working/building/REAL300004517411 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 447) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/447 `/scratch/stefan/7774842/working/3D/447' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1=CC=CC=N1)C(=O)C1=C(CC(=O)[O-])C2=CC=CC=C2N1) `REAL300004517411.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517411.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517411/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517411 none CN(CC1=CC=CC=N1)C(=O)C1=C(CC(=O)[O-])C2=CC=CC=C2N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [23, 9, 23, 66, 83, 83, 83, 83, 83, 1, 9, 1, 1, 1, 2, 7, 7, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 66, 66, 83, 83, 83, 83, 2, 2, 1, 1, 1, 1, 1] 85 rigid atoms, others: [35, 36, 37, 38, 39, 9, 11, 12, 13, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 296 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517411 none CN(CC1=CC=CC=N1)C(=O)C1=C(CC(=O)[O-])C2=CC=CC=C2N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [25, 8, 1, 1, 1, 1, 1, 1, 1, 25, 61, 61, 83, 83, 85, 85, 85, 83, 83, 83, 83, 83, 83, 83, 25, 25, 25, 8, 8, 1, 1, 1, 1, 85, 85, 83, 83, 83, 83, 83] 85 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517411 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517411 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517411/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517411 Building REAL300004517412 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517412' /scratch/stefan/7774842/working/building/REAL300004517412 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517412 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517412/0 /scratch/stefan/7774842/working/building/REAL300004517412 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 448) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/448 `/scratch/stefan/7774842/working/3D/448' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1=CC=CC=N1)C(=O)CN1C=C(C(=O)[O-])C2=CC=CC=C21) `REAL300004517412.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517412.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517412/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517412 none CN(CC1=CC=CC=N1)C(=O)CN1C=C(C(=O)[O-])C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [80, 30, 80, 183, 201, 201, 201, 201, 201, 8, 30, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 80, 80, 80, 183, 183, 201, 201, 201, 201, 8, 8, 1, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 39, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 743 number of broken/clashed sets: 71 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517412 none CN(CC1=CC=CC=N1)C(=O)CN1C=C(C(=O)[O-])C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 8, 1, 1, 1, 1, 1, 1, 1, 30, 70, 70, 139, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 30, 30, 30, 8, 8, 1, 1, 1, 1, 139, 139, 201, 201, 201, 201, 201] 201 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 624 number of broken/clashed sets: 71 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517412 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517412 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517412/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517412 Building REAL300004517413 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517413' /scratch/stefan/7774842/working/building/REAL300004517413 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517413 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517413/0 /scratch/stefan/7774842/working/building/REAL300004517413 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 449) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/449 `/scratch/stefan/7774842/working/3D/449' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1=CC=CC=N1)C(=O)C1=CC=C(C(=O)[O-])C=C1Cl) `REAL300004517413.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517413.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517413/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517413 none CN(CC1=CC=CC=N1)C(=O)C1=CC=C(C(=O)[O-])C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [25, 7, 25, 85, 126, 126, 126, 126, 126, 1, 7, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 25, 25, 25, 85, 85, 126, 126, 126, 126, 1, 1, 1] 126 rigid atoms, others: [32, 9, 11, 12, 13, 14, 15, 18, 19, 20, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 385 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517413 none CN(CC1=CC=CC=N1)C(=O)C1=CC=C(C(=O)[O-])C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 126 conformations in input total number of sets (complete confs): 126 using faster count positions algorithm for large data unique positions, atoms: [29, 9, 1, 1, 1, 1, 1, 1, 1, 29, 90, 90, 126, 126, 126, 126, 126, 126, 126, 126, 126, 29, 29, 29, 9, 9, 1, 1, 1, 1, 126, 126, 126] 126 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 26, 27, 28, 29] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32]) total number of confs: 326 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517413 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517413 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517413/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517413 Building REAL300004517414 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517414' /scratch/stefan/7774842/working/building/REAL300004517414 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517414 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517414/0 /scratch/stefan/7774842/working/building/REAL300004517414 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 450) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/450 `/scratch/stefan/7774842/working/3D/450' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)[O-])=NC(C(=O)N(C)CC2=CC=CC=N2)=C1) `REAL300004517414.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517414.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517414/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517414 none COC1=CC(C(=O)[O-])=NC(C(=O)N(C)CC2=CC=CC=N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 8, 1, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 3, 7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 174, 174, 174, 174, 174, 174, 174, 174, 97, 37, 97, 9, 37, 1, 1, 1, 1, 1, 1, 1, 174, 201, 201, 201, 174, 37, 37, 37, 9, 9, 1, 1, 1, 1, 174] 201 rigid atoms, others: [32, 33, 34, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35]) total number of confs: 441 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517414 none COC1=CC(C(=O)[O-])=NC(C(=O)N(C)CC2=CC=CC=N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 8, 1, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 3, 7, 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 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 8, 8, 34, 34, 103, 174, 174, 174, 174, 174, 1, 3, 3, 3, 1, 34, 34, 34, 103, 103, 174, 174, 174, 174, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 8, 9, 10, 35, 21, 25] set([0, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 493 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517414 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517414 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517414/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517414 Building REAL300004517415 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517415' /scratch/stefan/7774842/working/building/REAL300004517415 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517415 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517415/0 /scratch/stefan/7774842/working/building/REAL300004517415 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 451) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/451 `/scratch/stefan/7774842/working/3D/451' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1=CC=CC=N1)C(=O)C1CC2(C1)C(C(=O)[O-])C2(F)F) `REAL300004517415.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517415.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517415/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517415 none CN(CC1=CC=CC=N1)C(=O)C1CC2(C1)C(C(=O)[O-])C2(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [14, 6, 14, 48, 86, 86, 86, 86, 86, 1, 6, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 14, 14, 14, 48, 48, 86, 86, 86, 86, 1, 1, 1, 1, 1, 1] 86 rigid atoms, others: [32, 33, 34, 35, 36, 9, 11, 12, 13, 14, 15, 16, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 235 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517415 none CN(CC1=CC=CC=N1)C(=O)C1CC2(C1)C(C(=O)[O-])C2(F)F NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [35, 9, 1, 1, 1, 1, 1, 1, 1, 35, 70, 70, 86, 86, 86, 86, 86, 86, 86, 86, 86, 86, 35, 35, 35, 9, 9, 1, 1, 1, 1, 86, 86, 86, 86, 86, 86] 86 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 27, 28, 29, 30] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36]) total number of confs: 266 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517415 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517415 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517415/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517415 Building REAL300004517416 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517416' /scratch/stefan/7774842/working/building/REAL300004517416 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517416 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517416/0 /scratch/stefan/7774842/working/building/REAL300004517416 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 452) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/452 `/scratch/stefan/7774842/working/3D/452' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1=CC=CC=N1)C(=O)C1=CC2=C(SC(C(=O)[O-])=C2)S1) `REAL300004517416.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517416.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517416/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517416 none CN(CC1=CC=CC=N1)C(=O)C1=CC2=C(SC(C(=O)[O-])=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 14, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 11, 37, 132, 201, 201, 201, 201, 201, 1, 11, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 37, 37, 37, 132, 132, 201, 201, 201, 201, 1, 1] 201 rigid atoms, others: [32, 9, 11, 12, 13, 14, 15, 16, 17, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 604 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517416 none CN(CC1=CC=CC=N1)C(=O)C1=CC2=C(SC(C(=O)[O-])=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 14, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 9, 1, 1, 1, 1, 1, 1, 1, 35, 117, 117, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 35, 35, 35, 9, 9, 1, 1, 1, 1, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 27, 28, 29, 30] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32]) total number of confs: 485 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517416 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517416 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517416/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517416 Building REAL300004517417 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517417' /scratch/stefan/7774842/working/building/REAL300004517417 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517417 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517417/0 /scratch/stefan/7774842/working/building/REAL300004517417 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 453) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/453 `/scratch/stefan/7774842/working/3D/453' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)[O-])=C(Cl)C(C(=O)N(C)CC2=CC=CC=N2)=C1) `REAL300004517417.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517417.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517417/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517417 none COC1=CC(C(=O)[O-])=C(Cl)C(C(=O)N(C)CC2=CC=CC=N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 16, 1, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [187, 171, 171, 171, 171, 171, 181, 181, 171, 171, 98, 32, 98, 9, 32, 1, 1, 1, 1, 1, 1, 1, 171, 187, 187, 187, 171, 32, 32, 32, 9, 9, 1, 1, 1, 1, 171] 187 rigid atoms, others: [32, 33, 34, 35, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36]) total number of confs: 473 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517417 none COC1=CC(C(=O)[O-])=C(Cl)C(C(=O)N(C)CC2=CC=CC=N2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 16, 1, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 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 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 7, 7, 25, 25, 85, 171, 171, 171, 171, 171, 1, 2, 2, 2, 1, 25, 25, 25, 85, 85, 171, 171, 171, 171, 1] 187 rigid atoms, others: [1, 2, 3, 4, 5, 8, 9, 10, 11, 22, 36, 26] set([0, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 447 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517417 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517417 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517417/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517417 Building REAL300004517418 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517418' /scratch/stefan/7774842/working/building/REAL300004517418 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517418 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517418/0 /scratch/stefan/7774842/working/building/REAL300004517418 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 454) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/454 `/scratch/stefan/7774842/working/3D/454' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=CC(F)=C1C(=O)N(C)CC1=CC=CC=N1) `REAL300004517418.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517418.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517418/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517418 none CC1=C(C(=O)[O-])C=CC(F)=C1C(=O)N(C)CC1=CC=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [83, 83, 83, 83, 83, 83, 83, 83, 83, 83, 55, 23, 55, 7, 23, 1, 1, 1, 1, 1, 1, 1, 83, 83, 83, 83, 83, 23, 23, 23, 7, 7, 1, 1, 1, 1] 83 rigid atoms, others: [32, 33, 34, 35, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 210 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517418 none CC1=C(C(=O)[O-])C=CC(F)=C1C(=O)N(C)CC1=CC=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 15, 1, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 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] 0 hydrogens need rotated 83 conformations in input total number of sets (complete confs): 83 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 6, 6, 22, 22, 60, 83, 83, 83, 83, 83, 2, 2, 2, 1, 1, 23, 23, 23, 60, 60, 83, 83, 83, 83] 83 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 9, 10, 11, 25, 26] set([4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 284 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517418 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517418 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517418/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517418 Building REAL300004517419 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517419' /scratch/stefan/7774842/working/building/REAL300004517419 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517419 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517419/0 /scratch/stefan/7774842/working/building/REAL300004517419 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 455) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/455 `/scratch/stefan/7774842/working/3D/455' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1=CC=CC=N1)C(=O)C1=CC2=C(C(=O)[O-])C=CC=C2S1) `REAL300004517419.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517419 none CN(CC1=CC=CC=N1)C(=O)C1=CC2=C(C(=O)[O-])C=CC=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 11, 34, 119, 201, 201, 201, 201, 201, 1, 11, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 34, 34, 34, 119, 119, 201, 201, 201, 201, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 9, 11, 12, 13, 14, 15, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 561 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517419 none CN(CC1=CC=CC=N1)C(=O)C1=CC2=C(C(=O)[O-])C=CC=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 8, 1, 1, 1, 1, 1, 1, 1, 29, 92, 92, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 29, 29, 29, 8, 8, 1, 1, 1, 1, 201, 201, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 28, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35]) total number of confs: 424 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517419 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517419 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517419/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517419 Building REAL300004517420 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517420' /scratch/stefan/7774842/working/building/REAL300004517420 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517420 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517420/0 /scratch/stefan/7774842/working/building/REAL300004517420 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 456) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/456 `/scratch/stefan/7774842/working/3D/456' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1=CC=CC=N1)C(=O)C1=CC2=C(N1)C(C(=O)[O-])=CS2) `REAL300004517420.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517420.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517420/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517420 none CN(CC1=CC=CC=N1)C(=O)C1=CC2=C(N1)C(C(=O)[O-])=CS2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 11, 39, 139, 201, 201, 201, 201, 201, 1, 11, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 39, 39, 39, 139, 139, 201, 201, 201, 201, 1, 1, 1] 201 rigid atoms, others: [32, 33, 9, 11, 12, 13, 14, 15, 16, 17, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 621 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517420 none CN(CC1=CC=CC=N1)C(=O)C1=CC2=C(N1)C(C(=O)[O-])=CS2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 9, 1, 1, 1, 1, 1, 1, 1, 31, 105, 105, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 31, 31, 31, 9, 9, 1, 1, 1, 1, 201, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 27, 28, 29, 30] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33]) total number of confs: 446 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517420 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517420 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517420/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517420 Building REAL300004517421 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517421' /scratch/stefan/7774842/working/building/REAL300004517421 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517421 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517421/0 /scratch/stefan/7774842/working/building/REAL300004517421 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 457) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/457 `/scratch/stefan/7774842/working/3D/457' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1=CC=CC=N1)C(=O)C1=CC2=C(C=C(C(=O)[O-])S2)N1) `REAL300004517421.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517421.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517421/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517421 none CN(CC1=CC=CC=N1)C(=O)C1=CC2=C(C=C(C(=O)[O-])S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 11, 39, 145, 201, 201, 201, 201, 201, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 145, 145, 201, 201, 201, 201, 1, 1, 1] 201 rigid atoms, others: [32, 33, 9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 627 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517421 none CN(CC1=CC=CC=N1)C(=O)C1=CC2=C(C=C(C(=O)[O-])S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 9, 1, 1, 1, 1, 1, 1, 1, 33, 117, 117, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 33, 33, 33, 9, 9, 1, 1, 1, 1, 201, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 27, 28, 29, 30] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33]) total number of confs: 474 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517421 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517421 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517421/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517421 Building REAL300004517422 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517422' /scratch/stefan/7774842/working/building/REAL300004517422 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517422 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517422/0 /scratch/stefan/7774842/working/building/REAL300004517422 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 458) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/458 `/scratch/stefan/7774842/working/3D/458' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1=CC=CC=N1)C(=O)C1=CC=CC2=C(C(=O)[O-])C=CC=C12) `REAL300004517422.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517422 none CN(CC1=CC=CC=N1)C(=O)C1=CC=CC2=C(C(=O)[O-])C=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 185 conformations in input total number of sets (complete confs): 185 using faster count positions algorithm for large data unique positions, atoms: [25, 7, 25, 101, 185, 185, 185, 185, 185, 1, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 25, 25, 25, 101, 101, 185, 185, 185, 185, 1, 1, 1, 1, 1, 1] 185 rigid atoms, others: [33, 34, 35, 36, 37, 38, 9, 11, 12, 13, 14, 15, 16, 17, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 18, 19, 32, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 509 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517422 none CN(CC1=CC=CC=N1)C(=O)C1=CC=CC2=C(C(=O)[O-])C=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 185 conformations in input total number of sets (complete confs): 185 using faster count positions algorithm for large data unique positions, atoms: [33, 9, 1, 1, 1, 1, 1, 1, 1, 33, 101, 101, 185, 185, 185, 185, 185, 185, 185, 185, 185, 185, 185, 185, 33, 33, 33, 9, 9, 1, 1, 1, 1, 185, 185, 185, 185, 185, 185] 185 rigid atoms, others: [32, 2, 3, 4, 5, 6, 7, 8, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38]) total number of confs: 426 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517422 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517422 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517422/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517422 Building REAL300004517423 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517423' /scratch/stefan/7774842/working/building/REAL300004517423 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517423 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517423/0 /scratch/stefan/7774842/working/building/REAL300004517423 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 459) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/459 `/scratch/stefan/7774842/working/3D/459' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1=CC=CC=N1)C(=O)CC1=CC=C(C(=O)[O-])C(F)=C1) `REAL300004517423.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517423/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517423 none CN(CC1=CC=CC=N1)C(=O)CC1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [65, 23, 65, 173, 201, 201, 201, 201, 201, 7, 23, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 65, 65, 65, 173, 173, 201, 201, 201, 201, 7, 7, 1, 1, 1] 201 rigid atoms, others: [33, 34, 35, 11, 12, 13, 14, 15, 16, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 717 number of broken/clashed sets: 52 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517423 none CN(CC1=CC=CC=N1)C(=O)CC1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 8, 1, 1, 1, 1, 1, 1, 1, 25, 56, 56, 110, 201, 201, 201, 201, 201, 201, 201, 201, 201, 25, 25, 25, 8, 8, 1, 1, 1, 1, 110, 110, 201, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 27, 28, 29, 30] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35]) total number of confs: 573 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517423 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517423 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517423/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517423 Building REAL300004517424 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517424' /scratch/stefan/7774842/working/building/REAL300004517424 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517424 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517424/0 /scratch/stefan/7774842/working/building/REAL300004517424 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 460) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/460 `/scratch/stefan/7774842/working/3D/460' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1=CC=CC=N1)C(=O)C1=C2CCCCC2=C(C(=O)[O-])S1) `REAL300004517424.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517424.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517424/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517424 none CN(CC1=CC=CC=N1)C(=O)C1=C2CCCCC2=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 5, 5, 5, 5, 1, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 9, 29, 117, 201, 201, 201, 201, 201, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 29, 29, 29, 117, 117, 201, 201, 201, 201, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 554 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517424 none CN(CC1=CC=CC=N1)C(=O)C1=C2CCCCC2=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 5, 5, 5, 5, 1, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 9, 1, 1, 1, 1, 1, 1, 1, 32, 107, 107, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 201, 32, 32, 32, 9, 9, 1, 1, 1, 1, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 28, 29, 30, 31] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 445 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517424 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517424 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517424/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517424 Building REAL300004517425 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517425' /scratch/stefan/7774842/working/building/REAL300004517425 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517425 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517425/0 /scratch/stefan/7774842/working/building/REAL300004517425 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 461) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/461 `/scratch/stefan/7774842/working/3D/461' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC1=CC=CC=N1)C(=O)C12CCC(C(=O)[O-])(CC1)CC2) `REAL300004517425.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517425.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517425/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517425 none CN(CC1=CC=CC=N1)C(=O)C12CCC(C(=O)[O-])(CC1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [8, 4, 8, 9, 15, 15, 15, 15, 15, 1, 4, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 8, 8, 8, 9, 9, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 15 rigid atoms, others: [9, 11, 12, 13, 14, 15, 18, 19, 20, 21, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 47 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517425 none CN(CC1=CC=CC=N1)C(=O)C12CCC(C(=O)[O-])(CC1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [13, 7, 1, 1, 1, 1, 1, 1, 1, 13, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 13, 13, 13, 7, 7, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15] 15 rigid atoms, others: [2, 3, 4, 5, 6, 7, 8, 27, 28, 29, 30] set([0, 1, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 50 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517425 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517425 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517425/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517425 Building REAL300004517426 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517426' /scratch/stefan/7774842/working/building/REAL300004517426 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517426 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517426/0 /scratch/stefan/7774842/working/building/REAL300004517426 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 462) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/462 `/scratch/stefan/7774842/working/3D/462' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=CC=C(C(=O)[O-])C=C1) `REAL300004517426.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517426/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517426 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [117, 69, 41, 15, 4, 15, 43, 85, 85, 85, 85, 85, 1, 4, 1, 1, 1, 1, 1, 2, 2, 1, 1, 117, 117, 117, 69, 69, 41, 41, 43, 43, 85, 85, 85, 85, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 12, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 562 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517426 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [131, 89, 55, 25, 8, 1, 1, 1, 1, 1, 1, 1, 25, 75, 75, 85, 85, 75, 80, 85, 85, 85, 85, 131, 131, 131, 88, 88, 55, 55, 8, 8, 1, 1, 1, 1, 85, 85, 85, 85] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39]) total number of confs: 685 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517426 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517426 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517426/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517426 Building REAL300004517427 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517427' /scratch/stefan/7774842/working/building/REAL300004517427 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517427 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517427/0 /scratch/stefan/7774842/working/building/REAL300004517427 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 463) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/463 `/scratch/stefan/7774842/working/3D/463' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=CC=CC(OCC(=O)[O-])=C1) `REAL300004517427.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517427.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517427/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517427 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=CC(OCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 43, 31, 17, 7, 17, 33, 37, 37, 37, 37, 37, 1, 7, 1, 1, 1, 1, 1, 1, 6, 20, 33, 33, 1, 59, 59, 59, 43, 43, 31, 31, 33, 33, 37, 37, 37, 37, 1, 1, 1, 20, 20, 1] 201 rigid atoms, others: [38, 39, 40, 43, 12, 14, 15, 16, 17, 18, 19, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42]) total number of confs: 385 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517427 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=CC(OCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [47, 27, 17, 13, 8, 1, 1, 1, 1, 1, 1, 1, 13, 25, 25, 37, 37, 37, 37, 37, 93, 141, 151, 151, 37, 47, 47, 47, 26, 26, 17, 17, 8, 8, 1, 1, 1, 1, 37, 37, 37, 141, 141, 37] 201 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43]) total number of confs: 586 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517427 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517427 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517427/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517427 Building REAL300004517428 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517428' /scratch/stefan/7774842/working/building/REAL300004517428 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517428 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517428/0 /scratch/stefan/7774842/working/building/REAL300004517428 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 464) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/464 `/scratch/stefan/7774842/working/3D/464' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=CC=CC(C(=O)[O-])=C1) `REAL300004517428.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517428.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517428/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517428 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [144, 111, 73, 33, 11, 33, 90, 131, 131, 131, 131, 131, 1, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 144, 144, 144, 111, 111, 73, 73, 90, 90, 131, 131, 131, 131, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 12, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 874 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517428 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [116, 58, 38, 24, 8, 1, 1, 1, 1, 1, 1, 1, 24, 54, 54, 131, 131, 131, 131, 131, 131, 131, 131, 116, 116, 116, 57, 57, 38, 38, 8, 8, 1, 1, 1, 1, 131, 131, 131, 131] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39]) total number of confs: 538 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517428 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517428 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517428/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517428 Building REAL300004517429 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517429' /scratch/stefan/7774842/working/building/REAL300004517429 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517429 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517429/0 /scratch/stefan/7774842/working/building/REAL300004517429 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 465) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/465 `/scratch/stefan/7774842/working/3D/465' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=CC=C(C(=O)[O-])S1) `REAL300004517429.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517429.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517429/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517429 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [148, 124, 79, 29, 11, 29, 95, 141, 141, 141, 141, 141, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 148, 148, 148, 124, 124, 79, 79, 95, 95, 141, 141, 141, 141, 1, 1] 201 rigid atoms, others: [35, 36, 12, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 954 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517429 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [97, 59, 43, 25, 8, 1, 1, 1, 1, 1, 1, 1, 25, 63, 63, 141, 141, 141, 141, 141, 141, 141, 97, 97, 97, 58, 58, 43, 43, 8, 8, 1, 1, 1, 1, 141, 141] 201 rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36]) total number of confs: 544 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517429 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517429 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517429/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517429 Building REAL300004517430 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517430' /scratch/stefan/7774842/working/building/REAL300004517430 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517430 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517430/0 /scratch/stefan/7774842/working/building/REAL300004517430 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 466) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/466 `/scratch/stefan/7774842/working/3D/466' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=CC=CC(C(=O)[O-])=N1) `REAL300004517430.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517430.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517430/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517430 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=CC(C(=O)[O-])=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [38, 30, 27, 21, 8, 21, 31, 40, 40, 40, 40, 40, 1, 8, 1, 1, 1, 1, 1, 1, 2, 2, 1, 38, 38, 38, 30, 30, 27, 27, 31, 31, 40, 40, 40, 40, 1, 1, 1] 48 rigid atoms, others: [36, 37, 38, 12, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 183 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517430 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=CC(C(=O)[O-])=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [40, 35, 29, 19, 8, 1, 1, 1, 1, 1, 1, 1, 19, 27, 27, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 35, 35, 29, 29, 8, 8, 1, 1, 1, 1, 40, 40, 40] 48 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517430 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517430 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517430/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517430 Building REAL300004517431 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517431' /scratch/stefan/7774842/working/building/REAL300004517431 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517431 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517431/0 /scratch/stefan/7774842/working/building/REAL300004517431 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 467) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/467 `/scratch/stefan/7774842/working/3D/467' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=CC=CC=C1SC(C)C(=O)[O-]) `REAL300004517431.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517431.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517431/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517431 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=CC=C1SC(C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 14, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 5, 5, 4, 3, 4, 6, 6, 6, 6, 6, 6, 1, 3, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 5, 5, 5, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 2] 6 rigid atoms, others: [39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46]) total number of confs: 31 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517431 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=CC=C1SC(C)C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 14, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 4, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 4, 4, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6] 6 rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 10, 11, 38, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 21 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517431 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517431 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517431/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517431 Building REAL300004517432 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517432' /scratch/stefan/7774842/working/building/REAL300004517432 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517432 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517432/0 /scratch/stefan/7774842/working/building/REAL300004517432 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 468) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/468 `/scratch/stefan/7774842/working/3D/468' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C(=O)N(CCOC)CC2=CC=CC=N2)=CC=C1OCC(=O)[O-]) `REAL300004517432.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517432.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517432/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517432 none CCOC1=CC(C(=O)N(CCOC)CC2=CC=CC=N2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 12, 5, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 60, 28, 28, 28, 18, 10, 18, 7, 10, 18, 24, 42, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 71, 112, 123, 123, 71, 71, 71, 71, 71, 28, 18, 18, 24, 24, 42, 42, 42, 7, 7, 1, 1, 1, 1, 28, 28, 112, 112] 201 rigid atoms, others: [45, 43, 44, 13, 14, 15, 16, 17, 18, 19, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50]) total number of confs: 604 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517432 none CCOC1=CC(C(=O)N(CCOC)CC2=CC=CC=N2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 12, 5, 5, 1, 1, 1, 1, 1, 8, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [16, 7, 1, 1, 1, 1, 1, 7, 7, 13, 25, 37, 58, 13, 25, 28, 28, 28, 28, 28, 1, 1, 1, 1, 7, 15, 21, 21, 16, 16, 16, 16, 16, 1, 25, 25, 37, 37, 58, 58, 58, 25, 25, 28, 28, 28, 28, 1, 1, 15, 15] 201 rigid atoms, others: [33, 2, 3, 4, 5, 6, 47, 48, 20, 21, 22, 23] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 49, 50]) total number of confs: 355 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517432 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517432 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517432/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517432 Building REAL300004517433 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517433' /scratch/stefan/7774842/working/building/REAL300004517433 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517433 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517433/0 /scratch/stefan/7774842/working/building/REAL300004517433 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 469) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/469 `/scratch/stefan/7774842/working/3D/469' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)CCC1=CC=C(C(=O)[O-])C=C1) `REAL300004517433.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517433.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517433/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517433 none COCCN(CC1=CC=CC=N1)C(=O)CCC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [122, 96, 70, 42, 16, 42, 91, 131, 131, 131, 131, 131, 6, 16, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 122, 122, 122, 96, 96, 70, 70, 91, 91, 131, 131, 131, 131, 6, 6, 4, 4, 1, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 45, 15, 16, 17, 18, 19, 20, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 705 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517433 none COCCN(CC1=CC=CC=N1)C(=O)CCC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 73, 49, 27, 8, 1, 1, 1, 1, 1, 1, 1, 27, 71, 71, 122, 127, 131, 131, 127, 131, 131, 131, 131, 131, 99, 99, 99, 71, 71, 49, 49, 8, 8, 1, 1, 1, 1, 122, 122, 127, 127, 131, 131, 131, 131] 201 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 746 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517433 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517433 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517433/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517433 Building REAL300004517434 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517434' /scratch/stefan/7774842/working/building/REAL300004517434 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517434 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517434/0 /scratch/stefan/7774842/working/building/REAL300004517434 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 470) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/470 `/scratch/stefan/7774842/working/3D/470' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=CC=NC(C(=O)[O-])=C1) `REAL300004517434.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517434.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517434/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517434 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=NC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [152, 112, 70, 31, 11, 31, 91, 131, 131, 131, 131, 131, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 152, 152, 152, 112, 112, 70, 70, 91, 91, 131, 131, 131, 131, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 910 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517434 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=NC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [110, 56, 36, 24, 8, 1, 1, 1, 1, 1, 1, 1, 24, 59, 59, 131, 131, 131, 131, 131, 131, 131, 131, 110, 110, 110, 55, 55, 36, 36, 8, 8, 1, 1, 1, 1, 131, 131, 131] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38]) total number of confs: 543 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517434 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517434 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517434/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517434 Building REAL300004517435 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517435' /scratch/stefan/7774842/working/building/REAL300004517435 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517435 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517435/0 /scratch/stefan/7774842/working/building/REAL300004517435 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 471) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/471 `/scratch/stefan/7774842/working/3D/471' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C=CC1=CC=C(C(=O)[O-])C=C1) `REAL300004517435.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517435.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517435/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517435 none COCCN(CC1=CC=CC=N1)C(=O)C=CC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [147, 121, 73, 41, 16, 41, 93, 126, 126, 126, 126, 126, 3, 16, 3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 147, 147, 147, 121, 121, 73, 73, 93, 93, 126, 126, 126, 126, 3, 3, 1, 1, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 15, 16, 17, 18, 19, 20, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 886 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517435 none COCCN(CC1=CC=CC=N1)C(=O)C=CC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [89, 57, 39, 18, 8, 1, 1, 1, 1, 1, 1, 1, 18, 42, 42, 85, 85, 126, 126, 85, 85, 126, 126, 126, 126, 89, 89, 89, 56, 56, 39, 39, 8, 8, 1, 1, 1, 1, 87, 87, 126, 126, 126, 126] 201 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43]) total number of confs: 853 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517435 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517435 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517435/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517435 Building REAL300004517436 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517436' /scratch/stefan/7774842/working/building/REAL300004517436 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517436 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517436/0 /scratch/stefan/7774842/working/building/REAL300004517436 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 472) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/472 `/scratch/stefan/7774842/working/3D/472' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=CC(C(=O)[O-])=CC([N+](=O)[O-])=C1) `REAL300004517436.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517436.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517436/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517436 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC(C(=O)[O-])=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [144, 125, 75, 33, 11, 33, 95, 132, 132, 132, 132, 132, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 144, 144, 144, 125, 125, 75, 75, 95, 95, 132, 132, 132, 132, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 938 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517436 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC(C(=O)[O-])=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [87, 55, 33, 19, 7, 1, 1, 1, 1, 1, 1, 1, 19, 51, 51, 132, 132, 132, 132, 132, 132, 132, 132, 132, 132, 132, 87, 87, 87, 54, 54, 33, 33, 7, 7, 1, 1, 1, 1, 132, 132, 132] 201 rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 10, 11, 38, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41]) total number of confs: 509 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517436 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517436 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517436/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517436 Building REAL300004517437 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517437' /scratch/stefan/7774842/working/building/REAL300004517437 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517437 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517437/0 /scratch/stefan/7774842/working/building/REAL300004517437 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 473) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/473 `/scratch/stefan/7774842/working/3D/473' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=CC(C(=O)[O-])=CC([N+](=O)[O-])=C1) `REAL300004517437.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517437.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517437/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517437 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC(C(=O)[O-])=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [144, 125, 75, 33, 11, 33, 95, 132, 132, 132, 132, 132, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 144, 144, 144, 125, 125, 75, 75, 95, 95, 132, 132, 132, 132, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 938 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517437 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC(C(=O)[O-])=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [87, 55, 33, 19, 7, 1, 1, 1, 1, 1, 1, 1, 19, 51, 51, 132, 132, 132, 132, 132, 132, 132, 132, 132, 132, 132, 87, 87, 87, 54, 54, 33, 33, 7, 7, 1, 1, 1, 1, 132, 132, 132] 201 rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 10, 11, 38, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41]) total number of confs: 509 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517437 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517437 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517437/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517437 Building REAL300004517438 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517438' /scratch/stefan/7774842/working/building/REAL300004517438 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517438 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517438/0 /scratch/stefan/7774842/working/building/REAL300004517438 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 474) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/474 `/scratch/stefan/7774842/working/3D/474' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=CC=C(N2N=CC(C(=O)[O-])=C2C)C=C1) `REAL300004517438.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517438.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517438/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517438 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=C(N2N=CC(C(=O)[O-])=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 11, 11, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [43, 30, 18, 9, 4, 9, 22, 34, 34, 34, 34, 34, 1, 4, 1, 1, 1, 1, 1, 5, 5, 5, 5, 9, 9, 5, 5, 1, 1, 43, 43, 43, 30, 30, 18, 18, 22, 22, 34, 34, 34, 34, 1, 1, 5, 5, 5, 5, 1, 1] 201 rigid atoms, others: [48, 49, 42, 43, 12, 14, 15, 16, 17, 18, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 44, 45, 46, 47]) total number of confs: 262 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517438 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=C(N2N=CC(C(=O)[O-])=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 11, 11, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 38, 27, 19, 8, 1, 1, 1, 1, 1, 1, 1, 19, 34, 34, 34, 34, 34, 34, 123, 123, 123, 123, 143, 143, 123, 123, 34, 34, 52, 52, 52, 37, 37, 27, 27, 8, 8, 1, 1, 1, 1, 34, 34, 123, 123, 123, 123, 34, 34] 201 rigid atoms, others: [5, 38, 7, 8, 9, 10, 11, 40, 41, 39, 6] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 434 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517438 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=C(N2N=CC(C(=O)[O-])=C2C)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 8, 8, 1, 1, 1, 11, 11, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [140, 114, 66, 33, 13, 33, 82, 123, 123, 123, 123, 123, 1, 13, 1, 5, 5, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 5, 5, 140, 140, 140, 114, 114, 66, 66, 82, 82, 123, 123, 123, 123, 5, 5, 1, 2, 2, 2, 5, 5] 201 rigid atoms, others: [44, 17, 18, 19, 20, 21, 22, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47, 48, 49]) total number of confs: 898 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517438 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517438 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517438/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517438 Building REAL300004517439 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517439' /scratch/stefan/7774842/working/building/REAL300004517439 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517439 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517439/0 /scratch/stefan/7774842/working/building/REAL300004517439 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 475) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/475 `/scratch/stefan/7774842/working/3D/475' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=CC(C(=O)[O-])=NN1C1=CC=CC=C1) `REAL300004517439.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517439.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517439/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517439 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC(C(=O)[O-])=NN1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 11, 11, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [97, 64, 55, 25, 7, 25, 79, 147, 147, 147, 147, 147, 1, 7, 1, 1, 1, 1, 2, 2, 1, 1, 1, 5, 5, 2, 5, 5, 97, 97, 97, 64, 64, 55, 55, 79, 79, 147, 147, 147, 147, 1, 5, 5, 2, 5, 5] 201 rigid atoms, others: [41, 12, 14, 15, 16, 17, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44, 45, 46]) total number of confs: 649 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517439 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC(C(=O)[O-])=NN1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 11, 11, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [94, 60, 48, 29, 9, 1, 1, 1, 1, 1, 1, 1, 29, 77, 77, 147, 147, 147, 147, 147, 147, 147, 147, 174, 174, 168, 174, 174, 94, 94, 94, 59, 59, 48, 48, 9, 9, 1, 1, 1, 1, 147, 174, 174, 169, 174, 174] 201 rigid atoms, others: [37, 6, 7, 8, 9, 10, 11, 40, 39, 38, 5] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 46]) total number of confs: 621 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517439 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC(C(=O)[O-])=NN1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 11, 11, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [114, 83, 74, 45, 15, 45, 114, 174, 174, 174, 174, 174, 5, 15, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 114, 114, 114, 83, 83, 74, 74, 114, 114, 174, 174, 174, 174, 5, 1, 1, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 45, 46, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 755 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517439 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517439 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517439/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517439 Building REAL300004517440 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517440' /scratch/stefan/7774842/working/building/REAL300004517440 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517440 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517440/0 /scratch/stefan/7774842/working/building/REAL300004517440 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 476) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/476 `/scratch/stefan/7774842/working/3D/476' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=CC=C(C(=O)[O-])O1) `REAL300004517440.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517440/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517440 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 191 conformations in input total number of sets (complete confs): 191 using faster count positions algorithm for large data unique positions, atoms: [133, 100, 67, 29, 8, 29, 84, 136, 136, 136, 136, 136, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 133, 133, 133, 100, 100, 67, 67, 84, 84, 136, 136, 136, 136, 1, 1] 191 rigid atoms, others: [35, 36, 12, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 826 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517440 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 191 conformations in input total number of sets (complete confs): 191 using faster count positions algorithm for large data unique positions, atoms: [121, 77, 52, 23, 8, 1, 1, 1, 1, 1, 1, 1, 23, 75, 75, 136, 136, 136, 136, 136, 136, 136, 121, 121, 121, 76, 76, 52, 52, 8, 8, 1, 1, 1, 1, 136, 136] 191 rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36]) total number of confs: 640 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517440 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517440 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517440/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517440 Building REAL300004517441 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517441' /scratch/stefan/7774842/working/building/REAL300004517441 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517441 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517441/0 /scratch/stefan/7774842/working/building/REAL300004517441 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 477) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/477 `/scratch/stefan/7774842/working/3D/477' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)CCC1=CC=CC=C1C(=O)[O-]) `REAL300004517441.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517441.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517441/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517441 none COCCN(CC1=CC=CC=N1)C(=O)CCC1=CC=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 5, 5, 3, 5, 7, 7, 7, 7, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 9, 9, 9, 7, 7, 5, 5, 7, 7, 7, 7, 7, 7, 3, 3, 3, 3, 1, 1, 1, 1] 9 rigid atoms, others: [42, 43, 44, 45, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 50 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517441 none COCCN(CC1=CC=CC=N1)C(=O)CCC1=CC=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 7, 5, 3, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 9, 9, 9, 9, 7, 7, 3, 3, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7] 9 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 50 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517441 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517441 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517441/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517441 Building REAL300004517442 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517442' /scratch/stefan/7774842/working/building/REAL300004517442 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517442 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517442/0 /scratch/stefan/7774842/working/building/REAL300004517442 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 478) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/478 `/scratch/stefan/7774842/working/3D/478' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=CC(C)=C(OCC(=O)[O-])C(C)=C1) `REAL300004517442.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517442.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517442/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517442 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC(C)=C(OCC(=O)[O-])C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 5, 1, 12, 5, 1, 11, 11, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [86, 66, 41, 17, 7, 17, 41, 55, 55, 55, 55, 55, 1, 7, 1, 1, 1, 1, 1, 1, 2, 11, 18, 18, 1, 1, 1, 86, 86, 86, 66, 66, 41, 41, 41, 41, 55, 55, 55, 55, 1, 2, 2, 2, 11, 11, 2, 2, 2, 1] 201 rigid atoms, others: [49, 40, 12, 14, 15, 16, 17, 18, 19, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 533 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517442 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC(C)=C(OCC(=O)[O-])C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 5, 1, 12, 5, 1, 11, 11, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 36, 26, 15, 8, 1, 1, 1, 1, 1, 1, 1, 15, 31, 31, 55, 55, 55, 31, 31, 62, 131, 141, 141, 55, 55, 55, 53, 53, 53, 35, 35, 26, 26, 8, 8, 1, 1, 1, 1, 55, 55, 55, 55, 131, 131, 55, 55, 55, 55] 201 rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 11, 39, 38, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 761 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517442 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517442 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517442/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517442 Building REAL300004517443 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517443' /scratch/stefan/7774842/working/building/REAL300004517443 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517443 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517443/0 /scratch/stefan/7774842/working/building/REAL300004517443 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 479) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/479 `/scratch/stefan/7774842/working/3D/479' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)CC1=CC=CC(C(=O)[O-])=C1) `REAL300004517443.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517443.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517443/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517443 none COCCN(CC1=CC=CC=N1)C(=O)CC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [137, 119, 85, 55, 23, 55, 113, 137, 137, 137, 137, 137, 8, 23, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 137, 137, 137, 119, 119, 85, 85, 113, 113, 137, 137, 137, 137, 8, 8, 1, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 42, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 860 number of broken/clashed sets: 31 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517443 none COCCN(CC1=CC=CC=N1)C(=O)CC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [93, 61, 39, 23, 8, 1, 1, 1, 1, 1, 1, 1, 23, 55, 55, 117, 137, 137, 137, 137, 137, 137, 137, 137, 93, 93, 93, 60, 60, 39, 39, 8, 8, 1, 1, 1, 1, 117, 117, 137, 137, 137, 137] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42]) total number of confs: 699 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517443 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517443 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517443/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517443 Building REAL300004517444 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517444' /scratch/stefan/7774842/working/building/REAL300004517444 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517444 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517444/0 /scratch/stefan/7774842/working/building/REAL300004517444 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 480) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/480 `/scratch/stefan/7774842/working/3D/480' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1CCCC(C(=O)[O-])C1) `REAL300004517444.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517444.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517444/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517444 none COCCN(CC1=CC=CC=N1)C(=O)C1CCCC(C(=O)[O-])C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [21, 16, 10, 6, 4, 6, 14, 18, 18, 18, 18, 18, 1, 4, 1, 1, 1, 1, 1, 1, 3, 3, 1, 21, 21, 21, 16, 16, 10, 10, 14, 14, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 38 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 22, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 124 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517444 none COCCN(CC1=CC=CC=N1)C(=O)C1CCCC(C(=O)[O-])C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [35, 31, 19, 12, 7, 1, 1, 1, 1, 1, 1, 1, 12, 18, 18, 18, 18, 18, 18, 18, 25, 25, 18, 35, 35, 35, 29, 31, 19, 19, 7, 7, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18] 38 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 193 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517444 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517444 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517444/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517444 Building REAL300004517445 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517445' /scratch/stefan/7774842/working/building/REAL300004517445 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517445 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517445/0 /scratch/stefan/7774842/working/building/REAL300004517445 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 481) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/481 `/scratch/stefan/7774842/working/3D/481' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=CC=C(C(=O)[O-])N=C1) `REAL300004517445.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517445.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517445/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517445 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=C(C(=O)[O-])N=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [133, 98, 56, 21, 7, 21, 57, 98, 98, 98, 98, 98, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 133, 133, 133, 98, 98, 56, 56, 57, 57, 98, 98, 98, 98, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 720 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517445 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=C(C(=O)[O-])N=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 50, 36, 17, 8, 1, 1, 1, 1, 1, 1, 1, 17, 50, 50, 98, 98, 98, 98, 98, 98, 98, 98, 73, 73, 73, 49, 49, 36, 36, 8, 8, 1, 1, 1, 1, 98, 98, 98] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38]) total number of confs: 447 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517445 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517445 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517445/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517445 Building REAL300004517446 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517446' /scratch/stefan/7774842/working/building/REAL300004517446 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517446 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517446/0 /scratch/stefan/7774842/working/building/REAL300004517446 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 482) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/482 `/scratch/stefan/7774842/working/3D/482' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=CC=C(C(=O)[O-])C=N1) `REAL300004517446.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517446.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517446/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517446 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=C(C(=O)[O-])C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [125, 89, 61, 29, 9, 29, 71, 110, 110, 110, 110, 110, 1, 9, 1, 1, 1, 1, 1, 2, 2, 1, 1, 125, 125, 125, 89, 89, 61, 61, 71, 71, 110, 110, 110, 110, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 12, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 671 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517446 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=C(C(=O)[O-])C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [124, 85, 56, 25, 8, 1, 1, 1, 1, 1, 1, 1, 25, 71, 71, 110, 110, 110, 110, 110, 110, 110, 110, 124, 124, 124, 84, 85, 56, 56, 8, 8, 1, 1, 1, 1, 110, 110, 110] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38]) total number of confs: 651 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517446 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517446 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517446/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517446 Building REAL300004517447 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517447' /scratch/stefan/7774842/working/building/REAL300004517447 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517447 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517447/0 /scratch/stefan/7774842/working/building/REAL300004517447 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 483) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/483 `/scratch/stefan/7774842/working/3D/483' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)CC(C)(C)CC(=O)[O-]) `REAL300004517447.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517447.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517447/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517447 none COCCN(CC1=CC=CC=N1)C(=O)CC(C)(C)CC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [77, 45, 27, 17, 7, 1, 1, 1, 1, 1, 1, 1, 17, 25, 25, 37, 93, 93, 93, 139, 145, 145, 77, 77, 77, 44, 44, 27, 27, 7, 7, 1, 1, 1, 1, 37, 37, 93, 93, 93, 93, 93, 93, 139, 139] 201 rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 849 number of broken/clashed sets: 196 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517447 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517447 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517447/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517447 Building REAL300004517448 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517448' /scratch/stefan/7774842/working/building/REAL300004517448 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517448 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517448/0 /scratch/stefan/7774842/working/building/REAL300004517448 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 484) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/484 `/scratch/stefan/7774842/working/3D/484' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=CC=C(C(=O)[O-])C=C1F) `REAL300004517448.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517448.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517448/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517448 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=C(C(=O)[O-])C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [139, 104, 69, 23, 7, 23, 65, 97, 97, 97, 97, 97, 1, 7, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 139, 139, 139, 104, 104, 69, 69, 65, 65, 97, 97, 97, 97, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 12, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 776 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517448 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=C(C(=O)[O-])C=C1F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [105, 72, 52, 23, 8, 1, 1, 1, 1, 1, 1, 1, 23, 53, 53, 97, 97, 87, 97, 97, 97, 97, 97, 97, 105, 105, 105, 71, 71, 52, 52, 8, 8, 1, 1, 1, 1, 97, 97, 97] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39]) total number of confs: 582 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517448 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517448 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517448/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517448 Building REAL300004517449 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517449' /scratch/stefan/7774842/working/building/REAL300004517449 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517449 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517449/0 /scratch/stefan/7774842/working/building/REAL300004517449 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 485) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/485 `/scratch/stefan/7774842/working/3D/485' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=CN=C(C(=O)[O-])C=N1) `REAL300004517449.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517449/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517449 none COCCN(CC1=CC=CC=N1)C(=O)C1=CN=C(C(=O)[O-])C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 8, 1, 1, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 3, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [117, 81, 50, 26, 10, 26, 59, 103, 103, 103, 103, 103, 1, 10, 1, 1, 1, 1, 1, 2, 2, 1, 1, 117, 117, 117, 81, 81, 50, 50, 59, 59, 103, 103, 103, 103, 1, 1] 201 rigid atoms, others: [36, 37, 12, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 619 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517449 none COCCN(CC1=CC=CC=N1)C(=O)C1=CN=C(C(=O)[O-])C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 8, 1, 1, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 3, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [129, 92, 57, 27, 8, 1, 1, 1, 1, 1, 1, 1, 27, 75, 75, 103, 103, 103, 103, 103, 103, 103, 103, 129, 129, 129, 91, 91, 57, 57, 8, 8, 1, 1, 1, 1, 103, 103] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37]) total number of confs: 663 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517449 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517449 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517449/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517449 Building REAL300004517450 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517450' /scratch/stefan/7774842/working/building/REAL300004517450 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517450 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517450/0 /scratch/stefan/7774842/working/building/REAL300004517450 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 486) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/486 `/scratch/stefan/7774842/working/3D/486' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)[C@H]1CC[C@H](C(=O)[O-])CC1) `REAL300004517450.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517450.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517450/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517450 none COCCN(CC1=CC=CC=N1)C(=O)[C@H]1CC[C@H](C(=O)[O-])CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [98, 59, 36, 17, 6, 17, 40, 74, 74, 74, 74, 74, 1, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 98, 98, 98, 59, 59, 36, 36, 40, 40, 74, 74, 74, 74, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 20, 23, 24, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 499 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517450 none COCCN(CC1=CC=CC=N1)C(=O)[C@H]1CC[C@H](C(=O)[O-])CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [124, 74, 49, 26, 9, 1, 1, 1, 1, 1, 1, 1, 26, 56, 56, 74, 74, 74, 74, 74, 74, 116, 116, 74, 74, 124, 124, 124, 73, 73, 49, 49, 9, 9, 1, 1, 1, 1, 74, 74, 74, 74, 74, 74, 74, 74] 201 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 736 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517450 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517450 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517450/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517450 Building REAL300004517451 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517451' /scratch/stefan/7774842/working/building/REAL300004517451 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517451 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517451/0 /scratch/stefan/7774842/working/building/REAL300004517451 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 487) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/487 `/scratch/stefan/7774842/working/3D/487' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1CCC(C(=O)[O-])CC1) `REAL300004517451.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517451/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517451 none COCCN(CC1=CC=CC=N1)C(=O)C1CCC(C(=O)[O-])CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 1, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [100, 60, 36, 17, 6, 17, 40, 75, 75, 75, 75, 75, 1, 6, 1, 1, 1, 1, 1, 3, 3, 1, 1, 100, 100, 100, 60, 60, 36, 36, 40, 40, 75, 75, 75, 75, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 21, 22, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 505 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517451 none COCCN(CC1=CC=CC=N1)C(=O)C1CCC(C(=O)[O-])CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 1, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [124, 74, 48, 26, 9, 1, 1, 1, 1, 1, 1, 1, 26, 57, 57, 75, 75, 75, 75, 117, 117, 75, 75, 124, 124, 124, 73, 73, 48, 48, 9, 9, 1, 1, 1, 1, 75, 75, 75, 75, 75, 75, 75, 75, 75, 75] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 738 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517451 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517451 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517451/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517451 Building REAL300004517452 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517452' /scratch/stefan/7774842/working/building/REAL300004517452 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517452 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517452/0 /scratch/stefan/7774842/working/building/REAL300004517452 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 488) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/488 `/scratch/stefan/7774842/working/3D/488' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)CC1=CC=C(C(=O)[O-])C=C1) `REAL300004517452.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517452/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517452 none COCCN(CC1=CC=CC=N1)C(=O)CC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [127, 113, 77, 45, 14, 45, 107, 133, 133, 133, 133, 133, 4, 14, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 127, 127, 127, 113, 113, 77, 77, 107, 107, 133, 133, 133, 133, 4, 4, 1, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 42, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 821 number of broken/clashed sets: 38 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517452 none COCCN(CC1=CC=CC=N1)C(=O)CC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 75, 45, 27, 9, 1, 1, 1, 1, 1, 1, 1, 27, 61, 61, 123, 133, 133, 125, 133, 133, 133, 133, 133, 101, 101, 101, 73, 73, 45, 45, 9, 9, 1, 1, 1, 1, 123, 123, 133, 133, 133, 133] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42]) total number of confs: 786 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517452 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517452 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517452/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517452 Building REAL300004517453 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517453' /scratch/stefan/7774842/working/building/REAL300004517453 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517453 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517453/0 /scratch/stefan/7774842/working/building/REAL300004517453 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 489) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/489 `/scratch/stefan/7774842/working/3D/489' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)CN1C=C(C(=O)[O-])N=N1) `REAL300004517453.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517453/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517453 none COCCN(CC1=CC=CC=N1)C(=O)CN1C=C(C(=O)[O-])N=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 8, 1, 1, 1, 11, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [156, 145, 109, 93, 41, 93, 148, 163, 163, 163, 163, 163, 9, 41, 1, 1, 1, 1, 1, 2, 2, 1, 1, 156, 156, 156, 145, 145, 109, 109, 148, 148, 163, 163, 163, 163, 9, 9, 1] 201 rigid atoms, others: [38, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 856 number of broken/clashed sets: 27 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517453 none COCCN(CC1=CC=CC=N1)C(=O)CN1C=C(C(=O)[O-])N=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 8, 1, 1, 1, 11, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [62, 38, 30, 22, 8, 1, 1, 1, 1, 1, 1, 1, 22, 34, 34, 72, 163, 163, 163, 163, 163, 163, 163, 62, 62, 62, 38, 38, 30, 30, 8, 8, 1, 1, 1, 1, 72, 72, 163] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38]) total number of confs: 534 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517453 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517453 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517453/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517453 Building REAL300004517454 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517454' /scratch/stefan/7774842/working/building/REAL300004517454 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517454 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517454/0 /scratch/stefan/7774842/working/building/REAL300004517454 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 490) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/490 `/scratch/stefan/7774842/working/3D/490' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=CC=C(C(=O)[O-])C(C)=N1) `REAL300004517454.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517454.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517454/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517454 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=C(C(=O)[O-])C(C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [105, 57, 45, 23, 8, 23, 49, 83, 83, 83, 83, 83, 1, 8, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 105, 105, 105, 57, 57, 45, 45, 49, 49, 83, 83, 83, 83, 1, 1, 2, 2, 2] 201 rigid atoms, others: [37, 38, 12, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41]) total number of confs: 499 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517454 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=C(C(=O)[O-])C(C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [117, 67, 45, 23, 8, 1, 1, 1, 1, 1, 1, 1, 23, 59, 59, 83, 83, 83, 83, 119, 119, 83, 83, 83, 117, 117, 117, 67, 67, 45, 45, 8, 8, 1, 1, 1, 1, 83, 83, 83, 83, 83] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) total number of confs: 675 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517454 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517454 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517454/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517454 Building REAL300004517455 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517455' /scratch/stefan/7774842/working/building/REAL300004517455 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517455 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517455/0 /scratch/stefan/7774842/working/building/REAL300004517455 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 491) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/491 `/scratch/stefan/7774842/working/3D/491' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=CC(Br)=CC(C(=O)[O-])=C1) `REAL300004517455.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517455.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517455/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517455 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC(Br)=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 17, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [149, 119, 77, 33, 11, 33, 96, 132, 132, 132, 132, 132, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 149, 149, 149, 119, 119, 77, 77, 96, 96, 132, 132, 132, 132, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 931 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517455 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC(Br)=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 17, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [91, 51, 33, 19, 7, 1, 1, 1, 1, 1, 1, 1, 19, 48, 48, 132, 132, 132, 132, 132, 132, 132, 132, 132, 91, 91, 91, 50, 50, 33, 33, 7, 7, 1, 1, 1, 1, 132, 132, 132] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39]) total number of confs: 494 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517455 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517455 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517455/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517455 Building REAL300004517456 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517456' /scratch/stefan/7774842/working/building/REAL300004517456 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517456 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517456/0 /scratch/stefan/7774842/working/building/REAL300004517456 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 492) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/492 `/scratch/stefan/7774842/working/3D/492' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=CC=C(C(=O)[O-])C=C1) `REAL300004517456.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517456.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517456/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517456 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [117, 69, 41, 15, 4, 15, 43, 85, 85, 85, 85, 85, 1, 4, 1, 1, 1, 1, 1, 2, 2, 1, 1, 117, 117, 117, 69, 69, 41, 41, 43, 43, 85, 85, 85, 85, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 12, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 562 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517456 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [131, 89, 55, 25, 8, 1, 1, 1, 1, 1, 1, 1, 25, 75, 75, 85, 85, 75, 80, 85, 85, 85, 85, 131, 131, 131, 88, 88, 55, 55, 8, 8, 1, 1, 1, 1, 85, 85, 85, 85] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39]) total number of confs: 685 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517456 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517456 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517456/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517456 Building REAL300004517457 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517457' /scratch/stefan/7774842/working/building/REAL300004517457 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517457 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517457/0 /scratch/stefan/7774842/working/building/REAL300004517457 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 493) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/493 `/scratch/stefan/7774842/working/3D/493' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)[C@H]1CC[C@@H](C(=O)[O-])C1) `REAL300004517457.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517457/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517457 none COCCN(CC1=CC=CC=N1)C(=O)[C@H]1CC[C@@H](C(=O)[O-])C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [92, 67, 46, 22, 6, 22, 59, 99, 99, 99, 99, 99, 1, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 92, 92, 92, 67, 67, 46, 46, 59, 59, 99, 99, 99, 99, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 557 number of broken/clashed sets: 23 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517457 none COCCN(CC1=CC=CC=N1)C(=O)[C@H]1CC[C@@H](C(=O)[O-])C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [120, 78, 54, 28, 9, 1, 1, 1, 1, 1, 1, 1, 28, 66, 66, 99, 99, 99, 99, 99, 99, 128, 128, 99, 120, 120, 120, 77, 77, 54, 54, 9, 9, 1, 1, 1, 1, 99, 99, 99, 99, 99, 99] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42]) total number of confs: 726 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517457 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517457 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517457/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517457 Building REAL300004517458 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517458' /scratch/stefan/7774842/working/building/REAL300004517458 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517458 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517458/0 /scratch/stefan/7774842/working/building/REAL300004517458 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 494) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/494 `/scratch/stefan/7774842/working/3D/494' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=CC=CC(CC(=O)[O-])=C1) `REAL300004517458.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517458.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517458/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517458 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=CC(CC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [113, 76, 57, 27, 9, 27, 69, 117, 117, 117, 117, 117, 1, 9, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 113, 113, 113, 76, 76, 57, 57, 69, 69, 117, 117, 117, 117, 1, 1, 1, 2, 2, 1] 201 rigid atoms, others: [37, 38, 39, 42, 12, 14, 15, 16, 17, 18, 19, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41]) total number of confs: 663 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517458 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=CC(CC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [104, 71, 49, 25, 8, 1, 1, 1, 1, 1, 1, 1, 25, 71, 71, 117, 117, 95, 117, 117, 125, 142, 142, 117, 104, 104, 104, 71, 71, 49, 49, 8, 8, 1, 1, 1, 1, 117, 117, 111, 125, 125, 117] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42]) total number of confs: 783 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517458 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517458 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517458/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517458 Building REAL300004517459 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517459' /scratch/stefan/7774842/working/building/REAL300004517459 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517459 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517459/0 /scratch/stefan/7774842/working/building/REAL300004517459 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 495) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/495 `/scratch/stefan/7774842/working/3D/495' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=CC=CC=C1C1=CC=CC=C1C(=O)[O-]) `REAL300004517459.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517459 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=CC=C1C1=CC=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [46, 33, 23, 11, 7, 11, 27, 37, 37, 37, 37, 37, 1, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 2, 3, 3, 3, 5, 5, 46, 46, 46, 33, 33, 23, 23, 27, 27, 37, 37, 37, 37, 1, 1, 1, 1, 3, 3, 3, 3] 68 rigid atoms, others: [44, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48, 49]) total number of confs: 279 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517459 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=CC=C1C1=CC=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [57, 43, 27, 19, 9, 1, 1, 1, 1, 1, 1, 1, 19, 33, 33, 37, 37, 37, 37, 37, 37, 41, 41, 41, 41, 41, 41, 46, 46, 57, 57, 57, 43, 43, 27, 27, 9, 9, 1, 1, 1, 1, 37, 37, 37, 37, 41, 41, 41, 41] 68 rigid atoms, others: [5, 38, 7, 8, 9, 10, 11, 40, 41, 39, 6] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 303 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517459 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=CC=C1C1=CC=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [48, 35, 25, 15, 9, 15, 31, 41, 41, 41, 41, 41, 3, 9, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 48, 48, 48, 35, 35, 25, 25, 31, 31, 41, 41, 41, 41, 3, 3, 3, 3, 1, 1, 1, 1] 68 rigid atoms, others: [46, 47, 48, 49, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 276 number of broken/clashed sets: 0 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517459 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517459 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517459/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517459 Building REAL300004517460 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517460' /scratch/stefan/7774842/working/building/REAL300004517460 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517460 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517460/0 /scratch/stefan/7774842/working/building/REAL300004517460 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 496) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/496 `/scratch/stefan/7774842/working/3D/496' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=C(CC(=O)[O-])OC=C1) `REAL300004517460.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517460/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517460 none COCCN(CC1=CC=CC=N1)C(=O)C1=C(CC(=O)[O-])OC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 5, 1, 11, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [128, 91, 61, 27, 9, 27, 68, 112, 112, 112, 112, 112, 1, 9, 1, 1, 1, 2, 7, 7, 1, 1, 1, 128, 128, 128, 91, 91, 61, 61, 68, 68, 112, 112, 112, 112, 2, 2, 1, 1] 201 rigid atoms, others: [38, 39, 12, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 753 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517460 none COCCN(CC1=CC=CC=N1)C(=O)C1=C(CC(=O)[O-])OC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 5, 1, 11, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [120, 75, 51, 27, 9, 1, 1, 1, 1, 1, 1, 1, 27, 64, 64, 112, 112, 123, 144, 144, 112, 112, 112, 120, 120, 120, 74, 74, 51, 51, 9, 9, 1, 1, 1, 1, 123, 123, 112, 112] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39]) total number of confs: 734 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517460 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517460 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517460/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517460 Building REAL300004517461 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517461' /scratch/stefan/7774842/working/building/REAL300004517461 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517461 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517461/0 /scratch/stefan/7774842/working/building/REAL300004517461 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 497) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/497 `/scratch/stefan/7774842/working/3D/497' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=C(CC(=O)[O-])OC=C1C) `REAL300004517461.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517461/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517461 none COCCN(CC1=CC=CC=N1)C(=O)C1=C(CC(=O)[O-])OC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 5, 1, 11, 11, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [87, 66, 47, 27, 6, 26, 48, 61, 61, 61, 61, 61, 1, 6, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 87, 87, 87, 66, 66, 47, 47, 48, 48, 61, 61, 61, 61, 3, 3, 1, 2, 2, 2] 108 rigid atoms, others: [39, 12, 14, 15, 16, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42]) total number of confs: 473 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517461 none COCCN(CC1=CC=CC=N1)C(=O)C1=C(CC(=O)[O-])OC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 5, 1, 11, 11, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [66, 43, 27, 15, 7, 1, 1, 1, 1, 1, 1, 1, 15, 37, 37, 61, 61, 75, 79, 79, 61, 61, 61, 61, 66, 66, 66, 42, 42, 27, 27, 7, 7, 1, 1, 1, 1, 75, 75, 61, 61, 61, 61] 108 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42]) total number of confs: 439 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517461 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517461 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517461/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517461 Building REAL300004517462 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517462' /scratch/stefan/7774842/working/building/REAL300004517462 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517462 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517462/0 /scratch/stefan/7774842/working/building/REAL300004517462 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 498) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/498 `/scratch/stefan/7774842/working/3D/498' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=CC(C(=O)[O-])=CC=N1) `REAL300004517462.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517462/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517462 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC(C(=O)[O-])=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 173 conformations in input total number of sets (complete confs): 173 using faster count positions algorithm for large data unique positions, atoms: [129, 100, 76, 45, 12, 45, 100, 134, 134, 134, 134, 134, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 129, 129, 129, 100, 100, 76, 76, 100, 100, 134, 134, 134, 134, 1, 1, 1] 173 rigid atoms, others: [36, 37, 38, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 756 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517462 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC(C(=O)[O-])=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 173 conformations in input total number of sets (complete confs): 173 using faster count positions algorithm for large data unique positions, atoms: [97, 71, 51, 33, 9, 1, 1, 1, 1, 1, 1, 1, 33, 65, 65, 134, 134, 134, 134, 134, 134, 134, 134, 97, 97, 97, 71, 71, 51, 51, 9, 9, 1, 1, 1, 1, 134, 134, 134] 173 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38]) total number of confs: 540 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517462 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517462 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517462/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517462 Building REAL300004517463 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517463' /scratch/stefan/7774842/working/building/REAL300004517463 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517463 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517463/0 /scratch/stefan/7774842/working/building/REAL300004517463 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 499) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/499 `/scratch/stefan/7774842/working/3D/499' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C12CC(C(=O)[O-])(C1)C2) `REAL300004517463.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517463.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517463/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517463 none COCCN(CC1=CC=CC=N1)C(=O)C12CC(C(=O)[O-])(C1)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [94, 61, 42, 21, 7, 21, 52, 100, 100, 100, 100, 100, 1, 7, 1, 1, 1, 1, 3, 3, 1, 1, 94, 94, 94, 61, 61, 42, 42, 52, 52, 100, 100, 100, 100, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [35, 36, 37, 38, 39, 40, 12, 14, 15, 16, 17, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 528 number of broken/clashed sets: 112 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517463 none COCCN(CC1=CC=CC=N1)C(=O)C12CC(C(=O)[O-])(C1)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [156, 101, 63, 27, 9, 1, 1, 1, 1, 1, 1, 1, 27, 62, 62, 100, 100, 100, 138, 138, 100, 100, 156, 156, 156, 99, 99, 63, 63, 9, 9, 1, 1, 1, 1, 100, 100, 100, 100, 100, 100] 201 rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40]) total number of confs: 851 number of broken/clashed sets: 112 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517463 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517463 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517463/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517463 Building REAL300004517464 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517464' /scratch/stefan/7774842/working/building/REAL300004517464 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517464 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517464/0 /scratch/stefan/7774842/working/building/REAL300004517464 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 500) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/500 `/scratch/stefan/7774842/working/3D/500' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)CC1CCC(C(=O)[O-])CC1) `REAL300004517464.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517464/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517464 none COCCN(CC1=CC=CC=N1)C(=O)CC1CCC(C(=O)[O-])CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [99, 69, 41, 27, 13, 27, 61, 95, 95, 95, 95, 95, 5, 13, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 99, 99, 99, 69, 69, 41, 41, 61, 61, 95, 95, 95, 95, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [48, 39, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 46, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 562 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517464 none COCCN(CC1=CC=CC=N1)C(=O)CC1CCC(C(=O)[O-])CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [85, 51, 29, 19, 8, 1, 1, 1, 1, 1, 1, 1, 19, 41, 41, 77, 95, 95, 95, 95, 121, 121, 95, 95, 85, 85, 85, 49, 49, 29, 29, 8, 8, 1, 1, 1, 1, 77, 77, 95, 95, 95, 95, 95, 95, 95, 95, 95, 95] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 699 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517464 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517464 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517464/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517464 Building REAL300004517465 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517465' /scratch/stefan/7774842/working/building/REAL300004517465 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517465 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517465/0 /scratch/stefan/7774842/working/building/REAL300004517465 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 501) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/501 `/scratch/stefan/7774842/working/3D/501' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C12CCC(C(=O)[O-])(CC1)C2) `REAL300004517465.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517465 none COCCN(CC1=CC=CC=N1)C(=O)C12CCC(C(=O)[O-])(CC1)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 43, 25, 11, 4, 11, 31, 78, 78, 78, 78, 78, 1, 4, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 73, 73, 73, 43, 43, 25, 25, 31, 31, 78, 78, 78, 78, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 21, 22, 23, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 404 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517465 none COCCN(CC1=CC=CC=N1)C(=O)C12CCC(C(=O)[O-])(CC1)C2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [152, 97, 66, 31, 9, 1, 1, 1, 1, 1, 1, 1, 31, 54, 54, 78, 78, 78, 78, 122, 122, 78, 78, 78, 152, 152, 152, 97, 97, 66, 66, 9, 9, 1, 1, 1, 1, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 824 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517465 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517465 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517465/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517465 Building REAL300004517466 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517466' /scratch/stefan/7774842/working/building/REAL300004517466 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517466 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517466/0 /scratch/stefan/7774842/working/building/REAL300004517466 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 502) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/502 `/scratch/stefan/7774842/working/3D/502' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C12CCC(C(=O)[O-])(CC1)CC2) `REAL300004517466.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517466.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517466/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517466 none COCCN(CC1=CC=CC=N1)C(=O)C12CCC(C(=O)[O-])(CC1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [41, 27, 21, 9, 4, 9, 11, 13, 13, 13, 13, 13, 1, 4, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 41, 41, 41, 27, 27, 21, 21, 11, 11, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 43 rigid atoms, others: [12, 14, 15, 16, 17, 18, 21, 22, 23, 24, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 165 number of broken/clashed sets: 43 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517466 none COCCN(CC1=CC=CC=N1)C(=O)C12CCC(C(=O)[O-])(CC1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [39, 23, 17, 11, 7, 1, 1, 1, 1, 1, 1, 1, 11, 13, 13, 13, 13, 13, 13, 17, 17, 13, 13, 13, 13, 39, 39, 39, 23, 23, 17, 17, 7, 7, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 43 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 146 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517466 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517466 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517466/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517466 Building REAL300004517467 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517467' /scratch/stefan/7774842/working/building/REAL300004517467 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517467 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517467/0 /scratch/stefan/7774842/working/building/REAL300004517467 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 503) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/503 `/scratch/stefan/7774842/working/3D/503' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)CC(C)(C)CC(=O)[O-]) `REAL300004517467.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517467.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517467/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517467 none COCCN(CC1=CC=CC=N1)C(=O)CC(C)(C)CC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [77, 45, 27, 17, 7, 1, 1, 1, 1, 1, 1, 1, 17, 25, 25, 37, 93, 93, 93, 139, 145, 145, 77, 77, 77, 44, 44, 27, 27, 7, 7, 1, 1, 1, 1, 37, 37, 93, 93, 93, 93, 93, 93, 139, 139] 201 rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 849 number of broken/clashed sets: 196 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517467 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517467 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517467/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517467 Building REAL300004517468 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517468' /scratch/stefan/7774842/working/building/REAL300004517468 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517468 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517468/0 /scratch/stefan/7774842/working/building/REAL300004517468 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 504) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/504 `/scratch/stefan/7774842/working/3D/504' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=CC=NC2=C(C(=O)[O-])C=NN21) `REAL300004517468.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517468.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517468/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517468 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=NC2=C(C(=O)[O-])C=NN21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [111, 81, 57, 25, 7, 25, 67, 113, 113, 113, 113, 113, 1, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 111, 111, 111, 81, 81, 57, 57, 67, 67, 113, 113, 113, 113, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 12, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 669 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517468 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=NC2=C(C(=O)[O-])C=NN21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [127, 85, 55, 27, 8, 1, 1, 1, 1, 1, 1, 1, 27, 77, 77, 113, 113, 113, 113, 113, 113, 123, 123, 113, 113, 113, 127, 127, 127, 84, 84, 55, 55, 8, 8, 1, 1, 1, 1, 113, 113, 113] 201 rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 10, 11, 38, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41]) total number of confs: 673 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517468 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517468 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517468/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517468 Building REAL300004517469 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517469' /scratch/stefan/7774842/working/building/REAL300004517469 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517469 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517469/0 /scratch/stefan/7774842/working/building/REAL300004517469 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 505) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/505 `/scratch/stefan/7774842/working/3D/505' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=C(CC(=O)[O-])C2=CC=CC=C2N1) `REAL300004517469.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517469.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517469/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517469 none COCCN(CC1=CC=CC=N1)C(=O)C1=C(CC(=O)[O-])C2=CC=CC=C2N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [47, 34, 33, 17, 7, 17, 30, 55, 55, 55, 55, 55, 1, 7, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 34, 34, 33, 33, 30, 30, 55, 55, 55, 55, 3, 3, 1, 1, 1, 1, 1] 74 rigid atoms, others: [44, 42, 43, 12, 45, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 260 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517469 none COCCN(CC1=CC=CC=N1)C(=O)C1=C(CC(=O)[O-])C2=CC=CC=C2N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [65, 60, 54, 28, 9, 1, 1, 1, 1, 1, 1, 1, 28, 51, 51, 55, 55, 55, 60, 60, 55, 55, 55, 55, 55, 55, 55, 65, 65, 65, 60, 60, 54, 54, 9, 9, 1, 1, 1, 1, 55, 55, 55, 55, 55, 55, 55] 74 rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 11, 39, 38, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 361 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517469 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517469 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517469/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517469 Building REAL300004517470 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517470' /scratch/stefan/7774842/working/building/REAL300004517470 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517470 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517470/0 /scratch/stefan/7774842/working/building/REAL300004517470 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 506) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/506 `/scratch/stefan/7774842/working/3D/506' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=NOC(C(=O)[O-])=C1) `REAL300004517470.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517470 none COCCN(CC1=CC=CC=N1)C(=O)C1=NOC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 8, 12, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [146, 111, 81, 40, 12, 40, 104, 154, 154, 154, 154, 154, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 146, 146, 146, 111, 111, 81, 81, 104, 104, 154, 154, 154, 154, 1] 201 rigid atoms, others: [35, 12, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 891 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517470 none COCCN(CC1=CC=CC=N1)C(=O)C1=NOC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 8, 12, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 74, 50, 28, 9, 1, 1, 1, 1, 1, 1, 1, 28, 78, 78, 154, 154, 154, 154, 154, 154, 154, 101, 101, 101, 72, 72, 50, 50, 9, 9, 1, 1, 1, 1, 154] 201 rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35]) total number of confs: 622 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517470 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517470 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517470/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517470 Building REAL300004517471 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517471' /scratch/stefan/7774842/working/building/REAL300004517471 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517471 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517471/0 /scratch/stefan/7774842/working/building/REAL300004517471 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 507) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/507 `/scratch/stefan/7774842/working/3D/507' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1(C(=O)[O-])CCCC1) `REAL300004517471.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517471.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517471/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517471 none COCCN(CC1=CC=CC=N1)C(=O)C1(C(=O)[O-])CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 1, 11, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [15, 11, 7, 5, 3, 5, 12, 17, 17, 17, 17, 17, 1, 3, 1, 1, 3, 3, 1, 1, 1, 1, 15, 15, 15, 11, 11, 7, 7, 12, 12, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1] 20 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 12, 14, 15, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 104 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517471 none COCCN(CC1=CC=CC=N1)C(=O)C1(C(=O)[O-])CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 1, 11, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [19, 14, 12, 10, 7, 1, 1, 1, 1, 1, 1, 1, 10, 12, 12, 17, 17, 17, 17, 17, 17, 17, 19, 19, 19, 14, 14, 12, 12, 7, 7, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17] 20 rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 94 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517471 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517471 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517471/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517471 Building REAL300004517472 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517472' /scratch/stefan/7774842/working/building/REAL300004517472 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517472 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517472/0 /scratch/stefan/7774842/working/building/REAL300004517472 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 508) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/508 `/scratch/stefan/7774842/working/3D/508' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)CC1CCCC2=CC=C(C(=O)[O-])C=C21) `REAL300004517472.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517472.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517472/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517472 none COCCN(CC1=CC=CC=N1)C(=O)CC1CCCC2=CC=C(C(=O)[O-])C=C21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [126, 95, 73, 49, 15, 49, 100, 157, 157, 157, 157, 157, 4, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 126, 126, 126, 95, 95, 73, 73, 100, 100, 157, 157, 157, 157, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 777 number of broken/clashed sets: 103 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517472 none COCCN(CC1=CC=CC=N1)C(=O)CC1CCCC2=CC=C(C(=O)[O-])C=C21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [92, 61, 44, 25, 9, 1, 1, 1, 1, 1, 1, 1, 25, 77, 77, 140, 157, 157, 157, 157, 157, 157, 157, 157, 157, 157, 157, 157, 92, 92, 92, 61, 60, 44, 44, 9, 9, 1, 1, 1, 1, 140, 140, 157, 157, 157, 157, 157, 157, 157, 157, 157, 157] 201 rigid atoms, others: [37, 6, 7, 8, 9, 10, 11, 40, 39, 38, 5] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 811 number of broken/clashed sets: 103 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517472 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517472 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517472/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517472 Building REAL300004517473 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517473' /scratch/stefan/7774842/working/building/REAL300004517473 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517473 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517473/0 /scratch/stefan/7774842/working/building/REAL300004517473 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 509) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/509 `/scratch/stefan/7774842/working/3D/509' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=C(C)OC(C(=O)[O-])=C1) `REAL300004517473.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517473.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517473/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517473 none COCCN(CC1=CC=CC=N1)C(=O)C1=C(C)OC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 5, 12, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [137, 95, 59, 23, 9, 23, 74, 121, 121, 121, 121, 121, 1, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 137, 137, 137, 95, 95, 59, 59, 74, 74, 121, 121, 121, 121, 2, 2, 2, 1] 201 rigid atoms, others: [39, 12, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 799 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517473 none COCCN(CC1=CC=CC=N1)C(=O)C1=C(C)OC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 5, 12, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [115, 63, 45, 28, 8, 1, 1, 1, 1, 1, 1, 1, 28, 73, 73, 121, 121, 121, 121, 121, 121, 121, 121, 115, 115, 115, 62, 62, 45, 45, 8, 8, 1, 1, 1, 1, 121, 121, 121, 121] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39]) total number of confs: 545 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517473 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517473 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517473/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517473 Building REAL300004517474 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517474' /scratch/stefan/7774842/working/building/REAL300004517474 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517474 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517474/0 /scratch/stefan/7774842/working/building/REAL300004517474 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 510) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/510 `/scratch/stefan/7774842/working/3D/510' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=CC(C)=C(C(=O)[O-])O1) `REAL300004517474.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517474.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517474/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517474 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC(C)=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 5, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [121, 89, 64, 27, 8, 27, 71, 118, 118, 118, 118, 118, 1, 8, 1, 1, 1, 1, 1, 1, 2, 2, 1, 121, 121, 121, 89, 89, 64, 64, 71, 71, 118, 118, 118, 118, 1, 2, 2, 2] 201 rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39]) total number of confs: 723 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517474 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC(C)=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 5, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [122, 67, 47, 21, 8, 1, 1, 1, 1, 1, 1, 1, 21, 65, 65, 118, 118, 118, 118, 118, 147, 147, 118, 122, 122, 122, 66, 66, 47, 47, 8, 8, 1, 1, 1, 1, 118, 118, 118, 118] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39]) total number of confs: 695 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517474 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517474 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517474/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517474 Building REAL300004517475 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517475' /scratch/stefan/7774842/working/building/REAL300004517475 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517475 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517475/0 /scratch/stefan/7774842/working/building/REAL300004517475 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 511) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/511 `/scratch/stefan/7774842/working/3D/511' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)CN1C=C(C(=O)[O-])C=N1) `REAL300004517475.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517475/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517475 none COCCN(CC1=CC=CC=N1)C(=O)CN1C=C(C(=O)[O-])C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 8, 1, 1, 1, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [156, 144, 104, 91, 39, 91, 144, 159, 159, 159, 159, 159, 9, 39, 1, 1, 1, 1, 1, 1, 1, 1, 1, 156, 156, 156, 144, 144, 104, 104, 144, 144, 159, 159, 159, 159, 9, 9, 1, 1] 201 rigid atoms, others: [38, 39, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 842 number of broken/clashed sets: 20 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517475 none COCCN(CC1=CC=CC=N1)C(=O)CN1C=C(C(=O)[O-])C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 8, 1, 1, 1, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [62, 39, 31, 23, 8, 1, 1, 1, 1, 1, 1, 1, 23, 33, 33, 71, 159, 159, 159, 159, 159, 159, 159, 62, 62, 62, 39, 39, 31, 31, 8, 8, 1, 1, 1, 1, 71, 71, 159, 159] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39]) total number of confs: 527 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517475 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517475 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517475/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517475 Building REAL300004517476 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517476' /scratch/stefan/7774842/working/building/REAL300004517476 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517476 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517476/0 /scratch/stefan/7774842/working/building/REAL300004517476 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 512) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/512 `/scratch/stefan/7774842/working/3D/512' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=CC=C(C=CC(=O)[O-])O1) `REAL300004517476.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517476.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517476/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517476 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=C(C=CC(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [104, 76, 52, 26, 8, 26, 61, 97, 97, 97, 97, 97, 1, 8, 1, 1, 1, 1, 1, 8, 8, 14, 14, 1, 104, 104, 104, 76, 76, 52, 52, 61, 61, 97, 97, 97, 97, 1, 1, 8, 8] 201 rigid atoms, others: [37, 38, 12, 14, 15, 16, 17, 18, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40]) total number of confs: 629 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517476 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=C(C=CC(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [96, 55, 37, 21, 8, 1, 1, 1, 1, 1, 1, 1, 21, 59, 59, 97, 97, 97, 97, 154, 154, 158, 158, 97, 96, 96, 96, 54, 55, 37, 37, 8, 8, 1, 1, 1, 1, 97, 97, 154, 154] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40]) total number of confs: 670 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517476 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517476 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517476/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517476 Building REAL300004517477 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517477' /scratch/stefan/7774842/working/building/REAL300004517477 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517477 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517477/0 /scratch/stefan/7774842/working/building/REAL300004517477 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 513) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/513 `/scratch/stefan/7774842/working/3D/513' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1(C(=O)[O-])CC2(CCC2)C1) `REAL300004517477.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517477.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517477/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517477 none COCCN(CC1=CC=CC=N1)C(=O)C1(C(=O)[O-])CC2(CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 1, 11, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [12, 8, 7, 6, 3, 6, 11, 20, 20, 20, 20, 20, 1, 3, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 12, 12, 12, 8, 8, 7, 7, 11, 11, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 28 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 18, 19, 20, 21, 22, 23, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 78 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517477 none COCCN(CC1=CC=CC=N1)C(=O)C1(C(=O)[O-])CC2(CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 1, 11, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 24, 22, 15, 8, 1, 1, 1, 1, 1, 1, 1, 15, 20, 20, 20, 25, 25, 20, 20, 20, 20, 20, 20, 28, 28, 28, 24, 24, 22, 22, 8, 8, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20] 28 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517477 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517477 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517477/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517477 Building REAL300004517478 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517478' /scratch/stefan/7774842/working/building/REAL300004517478 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517478 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517478/0 /scratch/stefan/7774842/working/building/REAL300004517478 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 514) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/514 `/scratch/stefan/7774842/working/3D/514' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=CC=C(OCC(=O)[O-])C=C1) `REAL300004517478.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517478.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517478/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517478 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=C(OCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 27, 17, 9, 4, 9, 17, 23, 23, 23, 23, 23, 1, 4, 1, 1, 1, 1, 1, 6, 14, 23, 23, 1, 1, 37, 37, 37, 27, 27, 17, 17, 17, 17, 23, 23, 23, 23, 1, 1, 14, 14, 1, 1] 201 rigid atoms, others: [38, 39, 42, 43, 12, 14, 15, 16, 17, 18, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41]) total number of confs: 255 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517478 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=C(OCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [43, 31, 21, 13, 8, 1, 1, 1, 1, 1, 1, 1, 13, 23, 23, 23, 23, 23, 23, 69, 115, 125, 125, 23, 23, 43, 43, 43, 30, 30, 21, 21, 8, 8, 1, 1, 1, 1, 23, 23, 115, 115, 23, 23] 201 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43]) total number of confs: 541 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517478 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517478 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517478/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517478 Building REAL300004517479 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517479' /scratch/stefan/7774842/working/building/REAL300004517479 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517479 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517479/0 /scratch/stefan/7774842/working/building/REAL300004517479 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 515) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/515 `/scratch/stefan/7774842/working/3D/515' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1CC(C(=O)[O-])=NN1C1=CC=CC=C1) `REAL300004517479.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517479 none COCCN(CC1=CC=CC=N1)C(=O)C1CC(C(=O)[O-])=NN1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 1, 1, 11, 11, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [40, 31, 27, 18, 5, 18, 41, 52, 52, 52, 52, 52, 1, 5, 1, 1, 1, 1, 6, 6, 1, 1, 1, 5, 5, 3, 5, 5, 40, 40, 40, 31, 31, 27, 27, 41, 41, 52, 52, 52, 52, 1, 1, 1, 5, 5, 3, 5, 5] 65 rigid atoms, others: [41, 42, 43, 12, 14, 15, 16, 17, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 44, 45, 46, 47, 48]) total number of confs: 267 number of broken/clashed sets: 21 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517479 none COCCN(CC1=CC=CC=N1)C(=O)C1CC(C(=O)[O-])=NN1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 1, 1, 11, 11, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [52, 41, 32, 23, 8, 1, 1, 1, 1, 1, 1, 1, 23, 38, 38, 52, 52, 52, 54, 54, 52, 52, 52, 54, 54, 53, 54, 54, 52, 52, 52, 40, 41, 32, 32, 8, 8, 1, 1, 1, 1, 52, 52, 52, 54, 54, 53, 54, 54] 65 rigid atoms, others: [37, 6, 7, 8, 9, 10, 11, 40, 39, 38, 5] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 302 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517479 none COCCN(CC1=CC=CC=N1)C(=O)C1CC(C(=O)[O-])=NN1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 1, 1, 11, 11, 8, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [47, 39, 34, 26, 11, 26, 48, 54, 54, 54, 54, 54, 5, 11, 5, 5, 5, 5, 9, 9, 5, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 39, 39, 34, 34, 48, 48, 54, 54, 54, 54, 5, 5, 5, 1, 1, 1, 1, 1] 65 rigid atoms, others: [44, 45, 46, 47, 48, 21, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 283 number of broken/clashed sets: 21 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517479 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517479 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517479/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517479 Building REAL300004517480 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517480' /scratch/stefan/7774842/working/building/REAL300004517480 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517480 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517480/0 /scratch/stefan/7774842/working/building/REAL300004517480 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 516) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/516 `/scratch/stefan/7774842/working/3D/516' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)CCSCC(=O)[O-]) `REAL300004517480.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517480.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517480/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517480 none COCCN(CC1=CC=CC=N1)C(=O)CCSCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 14, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 137 conformations in input total number of sets (complete confs): 137 using faster count positions algorithm for large data unique positions, atoms: [63, 43, 29, 21, 8, 1, 1, 1, 1, 1, 1, 1, 21, 33, 33, 45, 49, 89, 109, 109, 109, 63, 63, 63, 42, 42, 29, 29, 8, 8, 1, 1, 1, 1, 45, 45, 49, 49, 109, 109] 137 rigid atoms, others: [32, 33, 5, 6, 7, 8, 9, 10, 11, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39]) total number of confs: 535 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517480 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517480 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517480/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517480 Building REAL300004517481 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517481' /scratch/stefan/7774842/working/building/REAL300004517481 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517481 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517481/0 /scratch/stefan/7774842/working/building/REAL300004517481 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 517) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/517 `/scratch/stefan/7774842/working/3D/517' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=CC=C(C(=O)[O-])C=N1) `REAL300004517481.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517481.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517481/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517481 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=C(C(=O)[O-])C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [125, 89, 61, 29, 9, 29, 71, 110, 110, 110, 110, 110, 1, 9, 1, 1, 1, 1, 1, 2, 2, 1, 1, 125, 125, 125, 89, 89, 61, 61, 71, 71, 110, 110, 110, 110, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 12, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 671 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517481 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=C(C(=O)[O-])C=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [124, 85, 56, 25, 8, 1, 1, 1, 1, 1, 1, 1, 25, 71, 71, 110, 110, 110, 110, 110, 110, 110, 110, 124, 124, 124, 84, 85, 56, 56, 8, 8, 1, 1, 1, 1, 110, 110, 110] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38]) total number of confs: 651 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517481 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517481 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517481/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517481 Building REAL300004517482 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517482' /scratch/stefan/7774842/working/building/REAL300004517482 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517482 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517482/0 /scratch/stefan/7774842/working/building/REAL300004517482 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 518) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/518 `/scratch/stefan/7774842/working/3D/518' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=CC(C(=O)[O-])=NN1C) `REAL300004517482.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517482/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517482 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC(C(=O)[O-])=NN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 11, 11, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 199 conformations in input total number of sets (complete confs): 199 using faster count positions algorithm for large data unique positions, atoms: [116, 82, 50, 21, 9, 21, 54, 105, 105, 105, 105, 105, 1, 9, 1, 1, 1, 1, 2, 2, 1, 1, 1, 116, 116, 116, 82, 82, 50, 50, 54, 54, 105, 105, 105, 105, 1, 2, 2, 2] 199 rigid atoms, others: [36, 12, 14, 15, 16, 17, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39]) total number of confs: 644 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517482 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC(C(=O)[O-])=NN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 11, 11, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 199 conformations in input total number of sets (complete confs): 199 using faster count positions algorithm for large data unique positions, atoms: [115, 73, 49, 23, 8, 1, 1, 1, 1, 1, 1, 1, 23, 66, 66, 105, 105, 105, 105, 105, 105, 105, 105, 115, 115, 115, 72, 71, 49, 49, 8, 8, 1, 1, 1, 1, 105, 105, 105, 105] 199 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39]) total number of confs: 570 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517482 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517482 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517482/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517482 Building REAL300004517483 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517483' /scratch/stefan/7774842/working/building/REAL300004517483 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517483 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517483/0 /scratch/stefan/7774842/working/building/REAL300004517483 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 519) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/519 `/scratch/stefan/7774842/working/3D/519' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)[C@H]1C[C@@H](C)[C@H](C(=O)[O-])O1) `REAL300004517483.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517483.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517483/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517483 none COCCN(CC1=CC=CC=N1)C(=O)[C@H]1C[C@@H](C)[C@H](C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 7, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [77, 48, 33, 20, 7, 20, 43, 69, 69, 69, 69, 69, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 77, 77, 77, 48, 48, 33, 33, 43, 43, 69, 69, 69, 69, 1, 1, 2, 2, 2] 130 rigid atoms, others: [39, 40, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43]) total number of confs: 394 number of broken/clashed sets: 19 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517483 none COCCN(CC1=CC=CC=N1)C(=O)[C@H]1C[C@@H](C)[C@H](C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 7, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 130 conformations in input total number of sets (complete confs): 130 using faster count positions algorithm for large data unique positions, atoms: [76, 50, 34, 21, 9, 1, 1, 1, 1, 1, 1, 1, 21, 42, 42, 69, 69, 69, 69, 69, 69, 69, 69, 88, 88, 69, 76, 76, 76, 50, 48, 34, 34, 9, 9, 1, 1, 1, 1, 69, 69, 69, 69, 69] 130 rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 10, 11, 38, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43]) total number of confs: 496 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517483 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517483 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517483/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517483 Building REAL300004517484 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517484' /scratch/stefan/7774842/working/building/REAL300004517484 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517484 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517484/0 /scratch/stefan/7774842/working/building/REAL300004517484 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 520) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/520 `/scratch/stefan/7774842/working/3D/520' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C(C)(C)CCC(=O)[O-]) `REAL300004517484.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517484/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517484 none COCCN(CC1=CC=CC=N1)C(=O)C(C)(C)CCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [49, 21, 13, 11, 7, 1, 1, 1, 1, 1, 1, 1, 11, 13, 13, 27, 27, 27, 79, 79, 107, 107, 49, 49, 49, 21, 21, 13, 13, 7, 7, 1, 1, 1, 1, 27, 27, 27, 27, 27, 27, 79, 79, 79, 79] 133 rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 552 number of broken/clashed sets: 133 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517484 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517484 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517484/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517484 Building REAL300004517485 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517485' /scratch/stefan/7774842/working/building/REAL300004517485 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517485 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517485/0 /scratch/stefan/7774842/working/building/REAL300004517485 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 521) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/521 `/scratch/stefan/7774842/working/3D/521' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=CC=C(CC(=O)[O-])C=C1) `REAL300004517485.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517485.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517485/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517485 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [96, 55, 35, 15, 4, 15, 51, 91, 91, 91, 91, 91, 1, 4, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 96, 96, 96, 55, 55, 35, 35, 51, 51, 91, 91, 91, 91, 1, 1, 2, 2, 1, 1] 201 rigid atoms, others: [37, 38, 41, 42, 12, 14, 15, 16, 17, 18, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40]) total number of confs: 542 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517485 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [103, 78, 56, 26, 9, 1, 1, 1, 1, 1, 1, 1, 26, 78, 78, 91, 91, 83, 85, 115, 129, 129, 91, 91, 103, 103, 103, 78, 78, 56, 56, 9, 9, 1, 1, 1, 1, 91, 91, 115, 115, 91, 91] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42]) total number of confs: 788 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517485 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517485 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517485/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517485 Building REAL300004517486 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517486' /scratch/stefan/7774842/working/building/REAL300004517486 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517486 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517486/0 /scratch/stefan/7774842/working/building/REAL300004517486 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 522) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/522 `/scratch/stefan/7774842/working/3D/522' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=CC=C(C=CC(=O)[O-])C=C1) `REAL300004517486.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517486.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517486/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517486 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=C(C=CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 47, 26, 10, 4, 10, 28, 46, 46, 46, 46, 46, 1, 4, 1, 1, 1, 1, 1, 5, 5, 9, 9, 1, 1, 71, 71, 71, 47, 47, 26, 26, 28, 28, 46, 46, 46, 46, 1, 1, 5, 5, 1, 1] 201 rigid atoms, others: [38, 39, 42, 43, 12, 14, 15, 16, 17, 18, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41]) total number of confs: 389 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517486 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=C(C=CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [79, 45, 33, 19, 8, 1, 1, 1, 1, 1, 1, 1, 19, 44, 44, 46, 46, 44, 44, 117, 117, 131, 131, 46, 46, 79, 79, 79, 44, 44, 33, 33, 8, 8, 1, 1, 1, 1, 46, 46, 117, 117, 46, 46] 201 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43]) total number of confs: 596 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517486 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517486 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517486/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517486 Building REAL300004517487 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517487' /scratch/stefan/7774842/working/building/REAL300004517487 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517487 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517487/0 /scratch/stefan/7774842/working/building/REAL300004517487 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 523) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/523 `/scratch/stefan/7774842/working/3D/523' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C=CC1=CC(C(=O)[O-])=CO1) `REAL300004517487.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517487.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517487/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517487 none COCCN(CC1=CC=CC=N1)C(=O)C=CC1=CC(C(=O)[O-])=CO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [162, 148, 110, 69, 31, 69, 126, 147, 147, 147, 147, 147, 6, 31, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 162, 162, 162, 148, 148, 110, 110, 126, 126, 147, 147, 147, 147, 6, 6, 1, 1] 201 rigid atoms, others: [39, 40, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 928 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517487 none COCCN(CC1=CC=CC=N1)C(=O)C=CC1=CC(C(=O)[O-])=CO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 47, 33, 21, 8, 1, 1, 1, 1, 1, 1, 1, 21, 44, 44, 104, 104, 147, 147, 147, 147, 147, 147, 146, 71, 71, 71, 46, 46, 33, 33, 8, 8, 1, 1, 1, 1, 104, 104, 147, 147] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40]) total number of confs: 538 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517487 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517487 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517487/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517487 Building REAL300004517488 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517488' /scratch/stefan/7774842/working/building/REAL300004517488 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517488 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517488/0 /scratch/stefan/7774842/working/building/REAL300004517488 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 524) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/524 `/scratch/stefan/7774842/working/3D/524' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=CC=CC=C1CCC(=O)[O-]) `REAL300004517488.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517488.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517488/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517488 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=CC=C1CCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 8, 5, 3, 5, 8, 8, 8, 8, 8, 8, 1, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 10, 10, 10, 10, 10, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 3, 3, 3, 3] 10 rigid atoms, others: [38, 39, 40, 41, 12, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45]) total number of confs: 66 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517488 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=CC=C1CCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 6, 5, 3, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 6, 3, 3, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8] 10 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 48 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517488 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517488 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517488/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517488 Building REAL300004517489 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517489' /scratch/stefan/7774842/working/building/REAL300004517489 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517489 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517489/0 /scratch/stefan/7774842/working/building/REAL300004517489 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 525) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/525 `/scratch/stefan/7774842/working/3D/525' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)COCC1=C(C(=O)[O-])N=CO1) `REAL300004517489.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517489/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517489 none COCCN(CC1=CC=CC=N1)C(=O)COCC1=C(C(=O)[O-])N=CO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 1, 11, 11, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [47, 42, 36, 24, 12, 24, 41, 47, 47, 47, 47, 47, 6, 12, 6, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 42, 42, 36, 36, 41, 41, 47, 47, 47, 47, 6, 6, 4, 4, 1] 49 rigid atoms, others: [42, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 269 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517489 none COCCN(CC1=CC=CC=N1)C(=O)COCC1=C(C(=O)[O-])N=CO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 1, 1, 1, 11, 11, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [27, 22, 19, 15, 8, 1, 1, 1, 1, 1, 1, 1, 15, 19, 19, 26, 29, 47, 47, 47, 47, 47, 47, 47, 47, 27, 27, 27, 22, 22, 19, 19, 8, 8, 1, 1, 1, 1, 26, 26, 47, 47, 47] 49 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 267 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517489 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517489 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517489/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517489 Building REAL300004517490 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517490' /scratch/stefan/7774842/working/building/REAL300004517490 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517490 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517490/0 /scratch/stefan/7774842/working/building/REAL300004517490 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 526) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/526 `/scratch/stefan/7774842/working/3D/526' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C=CC1=CC=C(C(=O)[O-])O1) `REAL300004517490.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517490.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517490/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517490 none COCCN(CC1=CC=CC=N1)C(=O)C=CC1=CC=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [148, 120, 90, 56, 27, 56, 106, 149, 149, 149, 149, 149, 8, 26, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 148, 148, 148, 120, 120, 90, 90, 106, 106, 149, 149, 149, 149, 8, 8, 1, 1] 201 rigid atoms, others: [39, 40, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 812 number of broken/clashed sets: 31 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517490 none COCCN(CC1=CC=CC=N1)C(=O)C=CC1=CC=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [100, 60, 37, 21, 8, 1, 1, 1, 1, 1, 1, 1, 21, 51, 51, 119, 119, 149, 149, 149, 149, 149, 149, 149, 100, 100, 100, 59, 59, 37, 37, 8, 8, 1, 1, 1, 1, 119, 119, 149, 149] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40]) total number of confs: 664 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517490 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517490 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517490/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517490 Building REAL300004517491 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517491' /scratch/stefan/7774842/working/building/REAL300004517491 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517491 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517491/0 /scratch/stefan/7774842/working/building/REAL300004517491 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 527) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/527 `/scratch/stefan/7774842/working/3D/527' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)[C@H]1CC[C@@H](C(=O)[O-])C1) `REAL300004517491.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517491.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517491/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517491 none COCCN(CC1=CC=CC=N1)C(=O)[C@H]1CC[C@@H](C(=O)[O-])C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [92, 67, 46, 22, 6, 22, 59, 99, 99, 99, 99, 99, 1, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 92, 92, 92, 67, 67, 46, 46, 59, 59, 99, 99, 99, 99, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 557 number of broken/clashed sets: 23 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517491 none COCCN(CC1=CC=CC=N1)C(=O)[C@H]1CC[C@@H](C(=O)[O-])C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [120, 78, 54, 28, 9, 1, 1, 1, 1, 1, 1, 1, 28, 66, 66, 99, 99, 99, 99, 99, 99, 128, 128, 99, 120, 120, 120, 77, 77, 54, 54, 9, 9, 1, 1, 1, 1, 99, 99, 99, 99, 99, 99] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42]) total number of confs: 726 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517491 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517491 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517491/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517491 Building REAL300004517492 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517492' /scratch/stefan/7774842/working/building/REAL300004517492 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517492 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517492/0 /scratch/stefan/7774842/working/building/REAL300004517492 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 528) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/528 `/scratch/stefan/7774842/working/3D/528' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=CC=C(C)C(C(=O)[O-])=C1) `REAL300004517492.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517492/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517492 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=C(C)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [140, 101, 65, 27, 9, 27, 62, 95, 95, 95, 95, 95, 1, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 140, 140, 140, 101, 101, 65, 65, 62, 62, 95, 95, 95, 95, 1, 1, 2, 2, 2, 1] 201 rigid atoms, others: [37, 38, 42, 12, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41]) total number of confs: 725 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517492 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=C(C)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [119, 75, 50, 22, 8, 1, 1, 1, 1, 1, 1, 1, 22, 62, 62, 95, 95, 95, 95, 95, 95, 95, 95, 95, 119, 119, 119, 74, 74, 50, 50, 8, 8, 1, 1, 1, 1, 95, 95, 95, 95, 95, 95] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42]) total number of confs: 564 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517492 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517492 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517492/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517492 Building REAL300004517493 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517493' /scratch/stefan/7774842/working/building/REAL300004517493 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517493 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517493/0 /scratch/stefan/7774842/working/building/REAL300004517493 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 529) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/529 `/scratch/stefan/7774842/working/3D/529' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=CN=CC(C(=O)[O-])=C1) `REAL300004517493.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517493/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517493 none COCCN(CC1=CC=CC=N1)C(=O)C1=CN=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 8, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [149, 115, 71, 32, 11, 32, 86, 134, 134, 134, 134, 134, 1, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 149, 149, 149, 115, 115, 71, 71, 86, 86, 134, 134, 134, 134, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 12, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 907 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517493 none COCCN(CC1=CC=CC=N1)C(=O)C1=CN=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 8, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 57, 39, 23, 8, 1, 1, 1, 1, 1, 1, 1, 23, 58, 58, 134, 134, 134, 134, 134, 134, 134, 134, 106, 106, 106, 56, 56, 39, 39, 8, 8, 1, 1, 1, 1, 134, 134, 134] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38]) total number of confs: 527 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517493 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517493 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517493/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517493 Building REAL300004517494 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517494' /scratch/stefan/7774842/working/building/REAL300004517494 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517494 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517494/0 /scratch/stefan/7774842/working/building/REAL300004517494 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 530) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/530 `/scratch/stefan/7774842/working/3D/530' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=CC(C(=O)[O-])=CN=C1C) `REAL300004517494.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517494 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC(C(=O)[O-])=CN=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 11, 11, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [123, 79, 47, 19, 7, 19, 64, 114, 114, 114, 114, 114, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 123, 123, 123, 79, 79, 47, 47, 64, 64, 114, 114, 114, 114, 1, 1, 2, 2, 2] 201 rigid atoms, others: [37, 38, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41]) total number of confs: 717 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517494 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC(C(=O)[O-])=CN=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 11, 11, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [120, 68, 46, 26, 9, 1, 1, 1, 1, 1, 1, 1, 26, 76, 76, 114, 114, 114, 114, 114, 114, 114, 114, 114, 120, 120, 120, 68, 68, 46, 46, 9, 9, 1, 1, 1, 1, 114, 114, 114, 114, 114] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) total number of confs: 592 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517494 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517494 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517494/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517494 Building REAL300004517495 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517495' /scratch/stefan/7774842/working/building/REAL300004517495 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517495 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517495/0 /scratch/stefan/7774842/working/building/REAL300004517495 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 531) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/531 `/scratch/stefan/7774842/working/3D/531' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)CN1C=CC(C(=O)[O-])=N1) `REAL300004517495.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517495 none COCCN(CC1=CC=CC=N1)C(=O)CN1C=CC(C(=O)[O-])=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 8, 1, 1, 1, 1, 11, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [142, 119, 93, 80, 37, 80, 136, 165, 165, 165, 165, 165, 9, 37, 1, 1, 1, 1, 1, 1, 2, 2, 1, 142, 142, 142, 119, 119, 93, 93, 136, 136, 165, 165, 165, 165, 9, 9, 1, 1] 201 rigid atoms, others: [38, 39, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 806 number of broken/clashed sets: 25 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517495 none COCCN(CC1=CC=CC=N1)C(=O)CN1C=CC(C(=O)[O-])=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 8, 1, 1, 1, 1, 11, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [72, 46, 33, 25, 8, 1, 1, 1, 1, 1, 1, 1, 25, 47, 47, 91, 165, 165, 165, 165, 165, 165, 165, 72, 72, 72, 46, 46, 33, 33, 8, 8, 1, 1, 1, 1, 91, 91, 165, 165] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39]) total number of confs: 619 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517495 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517495 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517495/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517495 Building REAL300004517496 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517496' /scratch/stefan/7774842/working/building/REAL300004517496 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517496 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517496/0 /scratch/stefan/7774842/working/building/REAL300004517496 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 532) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/532 `/scratch/stefan/7774842/working/3D/532' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)CCCN1C=CC(C(=O)[O-])=N1) `REAL300004517496.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517496.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517496/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517496 none COCCN(CC1=CC=CC=N1)C(=O)CCCN1C=CC(C(=O)[O-])=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 1, 11, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [109, 93, 79, 54, 27, 54, 97, 111, 111, 111, 111, 111, 15, 27, 11, 8, 1, 1, 1, 1, 1, 1, 2, 2, 1, 109, 109, 109, 93, 93, 79, 79, 97, 97, 111, 111, 111, 111, 15, 15, 11, 11, 8, 8, 1, 1] 143 rigid atoms, others: [44, 45, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 666 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517496 none COCCN(CC1=CC=CC=N1)C(=O)CCCN1C=CC(C(=O)[O-])=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 1, 11, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [61, 39, 31, 17, 6, 1, 1, 1, 1, 1, 1, 1, 17, 24, 24, 30, 48, 66, 111, 111, 111, 111, 111, 111, 111, 61, 61, 61, 39, 39, 31, 31, 6, 6, 1, 1, 1, 1, 30, 30, 48, 48, 66, 66, 111, 111] 143 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 518 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517496 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517496 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517496/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517496 Building REAL300004517497 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517497' /scratch/stefan/7774842/working/building/REAL300004517497 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517497 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517497/0 /scratch/stefan/7774842/working/building/REAL300004517497 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 533) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/533 `/scratch/stefan/7774842/working/3D/533' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)[C@H]1CC[C@@H](CCC(=O)[O-])O1) `REAL300004517497.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517497 none COCCN(CC1=CC=CC=N1)C(=O)[C@H]1CC[C@@H](CCC(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 5, 5, 7, 5, 5, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [92, 59, 34, 14, 5, 14, 35, 58, 58, 58, 58, 58, 1, 5, 1, 1, 1, 1, 1, 1, 1, 6, 9, 14, 14, 1, 92, 92, 92, 59, 59, 34, 34, 35, 35, 58, 58, 58, 58, 1, 1, 1, 1, 6, 6, 9, 9] 201 rigid atoms, others: [39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19, 20, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46]) total number of confs: 507 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517497 none COCCN(CC1=CC=CC=N1)C(=O)[C@H]1CC[C@@H](CCC(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 5, 5, 7, 5, 5, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [98, 56, 35, 18, 8, 1, 1, 1, 1, 1, 1, 1, 18, 43, 43, 58, 58, 58, 58, 58, 58, 116, 127, 133, 133, 58, 98, 98, 98, 56, 56, 35, 35, 8, 8, 1, 1, 1, 1, 58, 58, 58, 58, 116, 116, 127, 127] 201 rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 10, 11, 38, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 828 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517497 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517497 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517497/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517497 Building REAL300004517498 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517498' /scratch/stefan/7774842/working/building/REAL300004517498 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517498 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517498/0 /scratch/stefan/7774842/working/building/REAL300004517498 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 534) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/534 `/scratch/stefan/7774842/working/3D/534' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)CC[C@@H]1C[C@H](C(=O)[O-])CO1) `REAL300004517498.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517498 none COCCN(CC1=CC=CC=N1)C(=O)CC[C@@H]1C[C@H](C(=O)[O-])CO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 7, 5, 5, 7, 1, 11, 11, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 175 conformations in input total number of sets (complete confs): 175 using faster count positions algorithm for large data unique positions, atoms: [118, 97, 69, 39, 17, 39, 81, 109, 109, 109, 109, 109, 9, 17, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 118, 118, 118, 97, 97, 69, 69, 81, 81, 109, 109, 109, 109, 9, 9, 6, 6, 1, 1, 1, 1] 175 rigid atoms, others: [43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 713 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517498 none COCCN(CC1=CC=CC=N1)C(=O)CC[C@@H]1C[C@H](C(=O)[O-])CO1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 7, 5, 5, 7, 1, 11, 11, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 175 conformations in input total number of sets (complete confs): 175 using faster count positions algorithm for large data unique positions, atoms: [76, 42, 28, 20, 9, 1, 1, 1, 1, 1, 1, 1, 20, 34, 34, 56, 78, 109, 109, 109, 109, 109, 119, 119, 109, 109, 76, 76, 76, 42, 42, 28, 28, 9, 9, 1, 1, 1, 1, 56, 56, 81, 81, 109, 109, 109, 109] 175 rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 10, 11, 38, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 662 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517498 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517498 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517498/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517498 Building REAL300004517499 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517499' /scratch/stefan/7774842/working/building/REAL300004517499 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517499 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517499/0 /scratch/stefan/7774842/working/building/REAL300004517499 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 535) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/535 `/scratch/stefan/7774842/working/3D/535' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=C(C)C=C(C(=O)[O-])O1) `REAL300004517499.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517499.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517499/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517499 none COCCN(CC1=CC=CC=N1)C(=O)C1=C(C)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 5, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [142, 104, 70, 33, 8, 33, 84, 140, 140, 140, 140, 140, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 142, 142, 142, 104, 104, 70, 70, 84, 84, 140, 140, 140, 140, 2, 2, 2, 1] 201 rigid atoms, others: [39, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 821 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517499 none COCCN(CC1=CC=CC=N1)C(=O)C1=C(C)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 5, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [125, 73, 49, 23, 8, 1, 1, 1, 1, 1, 1, 1, 23, 73, 73, 140, 140, 140, 140, 140, 140, 140, 140, 125, 125, 125, 70, 70, 49, 49, 8, 8, 1, 1, 1, 1, 140, 140, 140, 140] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39]) total number of confs: 636 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517499 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517499 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517499/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517499 Building REAL300004517500 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517500' /scratch/stefan/7774842/working/building/REAL300004517500 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517500 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517500/0 /scratch/stefan/7774842/working/building/REAL300004517500 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 536) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/536 `/scratch/stefan/7774842/working/3D/536' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)[C@@H]1C2C=CC(CC2)[C@@H]1C(=O)[O-]) `REAL300004517500.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517500/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517500 none COCCN(CC1=CC=CC=N1)C(=O)[C@@H]1C2C=CC(CC2)[C@@H]1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 1, 1, 5, 5, 5, 5, 7, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [34, 23, 14, 7, 3, 7, 17, 26, 26, 26, 26, 26, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 34, 34, 34, 23, 23, 14, 14, 17, 17, 26, 26, 26, 26, 1, 1, 1, 1, 1, 1, 1, 1] 47 rigid atoms, others: [24, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 182 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517500 none COCCN(CC1=CC=CC=N1)C(=O)[C@@H]1C2C=CC(CC2)[C@@H]1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 1, 1, 5, 5, 5, 5, 7, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 47 conformations in input total number of sets (complete confs): 47 using default count positions algorithm for smaller data unique positions, atoms: [44, 39, 28, 18, 9, 1, 1, 1, 1, 1, 1, 1, 18, 24, 24, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 44, 44, 44, 39, 39, 28, 28, 9, 9, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26] 47 rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 11, 39, 38, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 204 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517500 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517500 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517500/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517500 Building REAL300004517501 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517501' /scratch/stefan/7774842/working/building/REAL300004517501 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517501 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517501/0 /scratch/stefan/7774842/working/building/REAL300004517501 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 537) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/537 `/scratch/stefan/7774842/working/3D/537' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)[C@H]1CCCC[C@H]1C(=O)[O-]) `REAL300004517501.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517501 none COCCN(CC1=CC=CC=N1)C(=O)[C@H]1CCCC[C@H]1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 5, 5, 5, 5, 7, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [30, 20, 13, 7, 4, 7, 19, 31, 31, 31, 31, 31, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 30, 30, 30, 20, 20, 13, 13, 19, 19, 31, 31, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1] 48 rigid atoms, others: [38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 187 number of broken/clashed sets: 20 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517501 none COCCN(CC1=CC=CC=N1)C(=O)[C@H]1CCCC[C@H]1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 5, 5, 5, 5, 7, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [43, 36, 26, 16, 8, 1, 1, 1, 1, 1, 1, 1, 16, 26, 26, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 43, 43, 43, 36, 36, 26, 26, 8, 8, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 31, 31] 48 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 223 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517501 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517501 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517501/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517501 Building REAL300004517502 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517502' /scratch/stefan/7774842/working/building/REAL300004517502 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300004517502 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517502/0 /scratch/stefan/7774842/working/building/REAL300004517502 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 538) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/538 `/scratch/stefan/7774842/working/3D/538' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C[N@@H+]1CCCC(C(=O)[O-])C1) `REAL300004517502.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517502/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517502 none COCCN(CC1=CC=CC=N1)C(=O)C[N@@H+]1CCCC(C(=O)[O-])C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 1, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [56, 46, 35, 25, 12, 25, 50, 63, 63, 63, 63, 63, 5, 12, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 56, 56, 56, 46, 46, 35, 35, 50, 50, 63, 63, 63, 63, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 85 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 24, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 368 number of broken/clashed sets: 85 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517502 none COCCN(CC1=CC=CC=N1)C(=O)C[N@@H+]1CCCC(C(=O)[O-])C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 1, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [46, 39, 26, 17, 8, 1, 1, 1, 1, 1, 1, 1, 17, 35, 35, 44, 63, 63, 63, 63, 63, 63, 70, 70, 63, 46, 46, 46, 39, 38, 26, 26, 8, 8, 1, 1, 1, 1, 44, 44, 63, 63, 63, 63, 63, 63, 63, 63, 63] 85 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 387 number of broken/clashed sets: 85 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517502 /scratch/stefan/7774842/working /scratch/stefan/7774842 mkdir: created directory `1' /scratch/stefan/7774842/working/building/REAL300004517502/1 /scratch/stefan/7774842/working/building/REAL300004517502 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 1 (index: 539) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/539 `/scratch/stefan/7774842/working/3D/539' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C[N@H+]1CCCC(C(=O)[O-])C1) `REAL300004517502.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004517502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517502/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517502 none COCCN(CC1=CC=CC=N1)C(=O)C[N@H+]1CCCC(C(=O)[O-])C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 1, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [62, 45, 34, 22, 10, 22, 42, 63, 63, 63, 63, 63, 6, 10, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 62, 62, 62, 45, 45, 34, 34, 42, 42, 63, 63, 63, 63, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1] 100 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 24, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 350 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517502 none COCCN(CC1=CC=CC=N1)C(=O)C[N@H+]1CCCC(C(=O)[O-])C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 1, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [79, 54, 40, 25, 8, 1, 1, 1, 1, 1, 1, 1, 25, 49, 49, 56, 63, 63, 63, 63, 63, 63, 72, 72, 63, 79, 79, 79, 54, 53, 40, 40, 8, 8, 1, 1, 1, 1, 56, 56, 63, 63, 63, 63, 63, 63, 63, 63, 63] 100 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 454 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517502 /scratch/stefan/7774842/working /scratch/stefan/7774842 mkdir: created directory `2' /scratch/stefan/7774842/working/building/REAL300004517502/2 /scratch/stefan/7774842/working/building/REAL300004517502 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 2 (index: 540) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/540 `/scratch/stefan/7774842/working/3D/540' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)CN1CCCC(C(=O)[O-])C1) `REAL300004517502.mol2' -> `2.mol2' `temp.mol2' -> `REAL300004517502.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517502/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517502 none COCCN(CC1=CC=CC=N1)C(=O)CN1CCCC(C(=O)[O-])C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 10, 5, 5, 5, 5, 1, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [108, 77, 47, 26, 9, 26, 59, 93, 93, 93, 93, 93, 5, 9, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 108, 108, 108, 77, 77, 47, 47, 59, 59, 93, 93, 93, 93, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 46, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 608 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517502 none COCCN(CC1=CC=CC=N1)C(=O)CN1CCCC(C(=O)[O-])C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 10, 5, 5, 5, 5, 1, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [117, 66, 43, 24, 8, 1, 1, 1, 1, 1, 1, 1, 24, 61, 61, 77, 93, 93, 93, 93, 93, 125, 125, 93, 117, 117, 117, 65, 66, 43, 43, 8, 8, 1, 1, 1, 1, 77, 77, 93, 93, 93, 93, 93, 93, 93, 93, 93] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 728 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517502 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517502 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 2: /scratch/stefan/7774842/working/building/REAL300004517502/2.* 1: /scratch/stefan/7774842/working/building/REAL300004517502/1.* 0: /scratch/stefan/7774842/working/building/REAL300004517502/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517502 Building REAL300004517503 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517503' /scratch/stefan/7774842/working/building/REAL300004517503 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517503 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517503/0 /scratch/stefan/7774842/working/building/REAL300004517503 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 541) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/541 `/scratch/stefan/7774842/working/3D/541' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1(C(=O)[O-])CC1C1=CC=CC=C1) `REAL300004517503.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517503 none COCCN(CC1=CC=CC=N1)C(=O)C1(C(=O)[O-])CC1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 1, 11, 11, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [19, 11, 9, 6, 3, 6, 16, 29, 29, 29, 29, 29, 1, 3, 1, 1, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 19, 19, 19, 11, 11, 9, 9, 16, 16, 29, 29, 29, 29, 1, 1, 1, 2, 2, 2, 2, 2] 35 rigid atoms, others: [39, 40, 41, 12, 14, 15, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44, 45, 46]) total number of confs: 126 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517503 none COCCN(CC1=CC=CC=N1)C(=O)C1(C(=O)[O-])CC1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 1, 11, 11, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [35, 33, 29, 23, 7, 1, 1, 1, 1, 1, 1, 1, 23, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 35, 35, 35, 33, 33, 29, 29, 7, 7, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29] 35 rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 10, 11, 38, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 149 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517503 none COCCN(CC1=CC=CC=N1)C(=O)C1(C(=O)[O-])CC1C1=CC=CC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 1, 11, 11, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [19, 11, 9, 6, 3, 6, 16, 29, 29, 29, 29, 29, 2, 3, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 11, 11, 9, 9, 16, 16, 29, 29, 29, 29, 2, 2, 2, 1, 1, 1, 1, 1] 35 rigid atoms, others: [42, 43, 44, 45, 46, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 122 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517503 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517503 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517503/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517503 Building REAL300004517504 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517504' /scratch/stefan/7774842/working/building/REAL300004517504 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517504 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517504/0 /scratch/stefan/7774842/working/building/REAL300004517504 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 542) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/542 `/scratch/stefan/7774842/working/3D/542' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=C(CC(=O)[O-])C2=CC=CC=C2N1) `REAL300004517504.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517504/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517504 none COCCN(CC1=CC=CC=N1)C(=O)C1=C(CC(=O)[O-])C2=CC=CC=C2N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [47, 34, 33, 17, 7, 17, 30, 55, 55, 55, 55, 55, 1, 7, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 34, 34, 33, 33, 30, 30, 55, 55, 55, 55, 3, 3, 1, 1, 1, 1, 1] 74 rigid atoms, others: [44, 42, 43, 12, 45, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 260 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517504 none COCCN(CC1=CC=CC=N1)C(=O)C1=C(CC(=O)[O-])C2=CC=CC=C2N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [65, 60, 54, 28, 9, 1, 1, 1, 1, 1, 1, 1, 28, 51, 51, 55, 55, 55, 60, 60, 55, 55, 55, 55, 55, 55, 55, 65, 65, 65, 60, 60, 54, 54, 9, 9, 1, 1, 1, 1, 55, 55, 55, 55, 55, 55, 55] 74 rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 11, 39, 38, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 361 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517504 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517504 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517504/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517504 Building REAL300004517505 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517505' /scratch/stefan/7774842/working/building/REAL300004517505 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517505 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517505/0 /scratch/stefan/7774842/working/building/REAL300004517505 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 543) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/543 `/scratch/stefan/7774842/working/3D/543' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)CN1C=C(C(=O)[O-])C2=CC=CC=C21) `REAL300004517505.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517505/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517505 none COCCN(CC1=CC=CC=N1)C(=O)CN1C=C(C(=O)[O-])C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [141, 135, 105, 79, 26, 79, 131, 155, 155, 155, 155, 155, 8, 26, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 141, 141, 141, 135, 135, 105, 105, 131, 131, 155, 155, 155, 155, 8, 8, 1, 1, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 45, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 812 number of broken/clashed sets: 39 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517505 none COCCN(CC1=CC=CC=N1)C(=O)CN1C=C(C(=O)[O-])C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [65, 49, 35, 25, 8, 1, 1, 1, 1, 1, 1, 1, 25, 43, 43, 103, 155, 155, 155, 155, 155, 155, 155, 155, 155, 155, 155, 65, 65, 65, 49, 49, 35, 35, 8, 8, 1, 1, 1, 1, 103, 103, 155, 155, 155, 155, 155] 201 rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 11, 39, 38, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 628 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517505 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517505 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517505/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517505 Building REAL300004517506 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517506' /scratch/stefan/7774842/working/building/REAL300004517506 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517506 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517506/0 /scratch/stefan/7774842/working/building/REAL300004517506 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 544) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/544 `/scratch/stefan/7774842/working/3D/544' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1CC2(CC2C(=O)[O-])C1) `REAL300004517506.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517506.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517506/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517506 none COCCN(CC1=CC=CC=N1)C(=O)C1CC2(CC2C(=O)[O-])C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 77, 53, 27, 7, 27, 59, 103, 103, 103, 103, 103, 1, 7, 1, 1, 1, 1, 1, 1, 3, 3, 1, 106, 106, 106, 77, 77, 53, 53, 59, 59, 103, 103, 103, 103, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 582 number of broken/clashed sets: 22 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517506 none COCCN(CC1=CC=CC=N1)C(=O)C1CC2(CC2C(=O)[O-])C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [111, 75, 49, 24, 9, 1, 1, 1, 1, 1, 1, 1, 24, 64, 64, 103, 103, 103, 103, 103, 128, 128, 103, 111, 111, 111, 74, 74, 49, 49, 9, 9, 1, 1, 1, 1, 103, 103, 103, 103, 103, 103, 103, 103] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 741 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517506 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517506 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517506/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517506 Building REAL300004517507 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517507' /scratch/stefan/7774842/working/building/REAL300004517507 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517507 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517507/0 /scratch/stefan/7774842/working/building/REAL300004517507 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 545) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/545 `/scratch/stefan/7774842/working/3D/545' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)[C@H]1C[C@]1(C(=O)[O-])C(C)C) `REAL300004517507.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517507 none COCCN(CC1=CC=CC=N1)C(=O)[C@H]1C[C@]1(C(=O)[O-])C(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [55, 35, 21, 11, 5, 11, 23, 41, 41, 41, 41, 41, 1, 5, 1, 1, 1, 1, 1, 2, 2, 1, 8, 8, 55, 55, 55, 35, 35, 21, 21, 23, 23, 41, 41, 41, 41, 1, 1, 8, 8, 8, 8, 8, 8, 8] 119 rigid atoms, others: [37, 38, 12, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 308 number of broken/clashed sets: 40 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517507 none COCCN(CC1=CC=CC=N1)C(=O)[C@H]1C[C@]1(C(=O)[O-])C(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 119 conformations in input total number of sets (complete confs): 119 using faster count positions algorithm for large data unique positions, atoms: [75, 44, 27, 16, 8, 1, 1, 1, 1, 1, 1, 1, 16, 22, 22, 41, 41, 41, 41, 41, 41, 41, 80, 80, 75, 75, 75, 44, 43, 27, 27, 8, 8, 1, 1, 1, 1, 41, 41, 80, 80, 80, 80, 80, 80, 80] 119 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 521 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517507 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517507 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517507/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517507 Building REAL300004517508 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517508' /scratch/stefan/7774842/working/building/REAL300004517508 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517508 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517508/0 /scratch/stefan/7774842/working/building/REAL300004517508 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 546) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/546 `/scratch/stefan/7774842/working/3D/546' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=CC(C(=O)[O-])=CC=C1C) `REAL300004517508.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517508.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517508/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517508 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC(C(=O)[O-])=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [115, 78, 47, 19, 7, 19, 69, 112, 112, 112, 112, 112, 1, 7, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 115, 115, 115, 78, 78, 47, 47, 69, 69, 112, 112, 112, 112, 1, 1, 1, 2, 2, 2] 201 rigid atoms, others: [37, 38, 39, 12, 14, 15, 16, 17, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42]) total number of confs: 710 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517508 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC(C(=O)[O-])=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [124, 70, 46, 26, 9, 1, 1, 1, 1, 1, 1, 1, 26, 73, 73, 112, 112, 112, 112, 112, 112, 112, 112, 112, 124, 124, 124, 70, 70, 46, 46, 9, 9, 1, 1, 1, 1, 112, 112, 112, 112, 112, 112] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42]) total number of confs: 609 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517508 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517508 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517508/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517508 Building REAL300004517509 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517509' /scratch/stefan/7774842/working/building/REAL300004517509 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517509 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517509/0 /scratch/stefan/7774842/working/building/REAL300004517509 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 547) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/547 `/scratch/stefan/7774842/working/3D/547' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1CC(C)(C(=O)[O-])C1) `REAL300004517509.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517509.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517509/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517509 none COCCN(CC1=CC=CC=N1)C(=O)C1CC(C)(C(=O)[O-])C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 1, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [119, 78, 51, 26, 8, 26, 57, 86, 86, 86, 86, 86, 1, 8, 1, 1, 1, 1, 1, 3, 3, 1, 119, 119, 119, 78, 78, 51, 51, 57, 57, 86, 86, 86, 86, 1, 1, 1, 2, 2, 2, 1, 1] 201 rigid atoms, others: [35, 36, 37, 41, 42, 12, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40]) total number of confs: 607 number of broken/clashed sets: 34 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517509 none COCCN(CC1=CC=CC=N1)C(=O)C1CC(C)(C(=O)[O-])C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 1, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [97, 54, 39, 19, 9, 1, 1, 1, 1, 1, 1, 1, 19, 48, 48, 86, 86, 86, 86, 120, 120, 86, 97, 97, 97, 54, 54, 39, 39, 9, 9, 1, 1, 1, 1, 86, 86, 86, 86, 86, 86, 86, 86] 201 rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 654 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517509 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517509 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517509/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517509 Building REAL300004517510 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517510' /scratch/stefan/7774842/working/building/REAL300004517510 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517510 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517510/0 /scratch/stefan/7774842/working/building/REAL300004517510 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 548) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/548 `/scratch/stefan/7774842/working/3D/548' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=C(C(=O)[O-])SC=C1) `REAL300004517510.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517510.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517510/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517510 none COCCN(CC1=CC=CC=N1)C(=O)C1=C(C(=O)[O-])SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 11, 11, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [108, 77, 53, 25, 7, 25, 54, 89, 89, 89, 89, 89, 1, 7, 1, 1, 1, 3, 3, 1, 1, 1, 108, 108, 108, 77, 77, 53, 53, 54, 54, 89, 89, 89, 89, 1, 1] 201 rigid atoms, others: [35, 36, 12, 14, 15, 16, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 562 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517510 none COCCN(CC1=CC=CC=N1)C(=O)C1=C(C(=O)[O-])SC=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 11, 11, 14, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [134, 76, 50, 27, 9, 1, 1, 1, 1, 1, 1, 1, 27, 62, 62, 89, 89, 114, 114, 89, 89, 89, 134, 134, 134, 76, 76, 50, 50, 9, 9, 1, 1, 1, 1, 89, 89] 201 rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36]) total number of confs: 681 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517510 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517510 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517510/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517510 Building REAL300004517511 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517511' /scratch/stefan/7774842/working/building/REAL300004517511 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517511 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517511/0 /scratch/stefan/7774842/working/building/REAL300004517511 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 549) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/549 `/scratch/stefan/7774842/working/3D/549' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=CC(C(=O)[O-])=NN1) `REAL300004517511.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517511 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC(C(=O)[O-])=NN1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 11, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 152 conformations in input total number of sets (complete confs): 152 using faster count positions algorithm for large data unique positions, atoms: [117, 84, 51, 19, 11, 19, 63, 96, 96, 96, 96, 96, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 117, 117, 117, 84, 84, 51, 51, 63, 63, 96, 96, 96, 96, 1, 1] 152 rigid atoms, others: [35, 36, 12, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 681 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517511 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC(C(=O)[O-])=NN1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 11, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 152 conformations in input total number of sets (complete confs): 152 using faster count positions algorithm for large data unique positions, atoms: [86, 53, 39, 21, 8, 1, 1, 1, 1, 1, 1, 1, 21, 56, 56, 96, 96, 96, 96, 96, 96, 96, 86, 86, 86, 52, 52, 39, 39, 8, 8, 1, 1, 1, 1, 96, 96] 152 rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36]) total number of confs: 448 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517511 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517511 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517511/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517511 Building REAL300004517512 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517512' /scratch/stefan/7774842/working/building/REAL300004517512 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517512 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517512/0 /scratch/stefan/7774842/working/building/REAL300004517512 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 550) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/550 `/scratch/stefan/7774842/working/3D/550' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=CN=CC(C(=O)[O-])=C1C) `REAL300004517512.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517512/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517512 none COCCN(CC1=CC=CC=N1)C(=O)C1=CN=CC(C(=O)[O-])=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 8, 1, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [131, 92, 58, 21, 7, 21, 67, 107, 107, 107, 107, 107, 1, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 131, 131, 131, 92, 92, 58, 58, 67, 67, 107, 107, 107, 107, 1, 1, 2, 2, 2] 201 rigid atoms, others: [37, 38, 12, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41]) total number of confs: 753 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517512 none COCCN(CC1=CC=CC=N1)C(=O)C1=CN=CC(C(=O)[O-])=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 8, 1, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [120, 80, 53, 25, 9, 1, 1, 1, 1, 1, 1, 1, 25, 70, 70, 107, 107, 107, 107, 107, 107, 107, 107, 107, 120, 120, 120, 79, 79, 53, 53, 9, 9, 1, 1, 1, 1, 107, 107, 107, 107, 107] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41]) total number of confs: 608 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517512 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517512 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517512/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517512 Building REAL300004517513 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517513' /scratch/stefan/7774842/working/building/REAL300004517513 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517513 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517513/0 /scratch/stefan/7774842/working/building/REAL300004517513 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 551) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/551 `/scratch/stefan/7774842/working/3D/551' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=CC=C(C(=O)[O-])C=C1C) `REAL300004517513.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517513.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517513/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517513 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [130, 84, 50, 19, 7, 19, 57, 97, 97, 97, 97, 97, 1, 7, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 130, 130, 130, 84, 84, 50, 50, 57, 57, 97, 97, 97, 97, 1, 1, 1, 2, 2, 2] 201 rigid atoms, others: [37, 38, 39, 12, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42]) total number of confs: 683 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517513 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [119, 81, 55, 25, 9, 1, 1, 1, 1, 1, 1, 1, 25, 70, 70, 97, 97, 94, 94, 97, 97, 97, 97, 97, 119, 119, 119, 81, 81, 55, 55, 9, 9, 1, 1, 1, 1, 97, 97, 97, 97, 97, 97] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42]) total number of confs: 622 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517513 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517513 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517513/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517513 Building REAL300004517514 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517514' /scratch/stefan/7774842/working/building/REAL300004517514 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517514 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517514/0 /scratch/stefan/7774842/working/building/REAL300004517514 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 552) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/552 `/scratch/stefan/7774842/working/3D/552' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=CC=C(C(=O)[O-])C=C1Cl) `REAL300004517514.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517514.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517514/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517514 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=C(C(=O)[O-])C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [133, 93, 55, 21, 7, 21, 65, 101, 101, 101, 101, 101, 1, 7, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 133, 133, 133, 93, 93, 55, 55, 65, 65, 101, 101, 101, 101, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 12, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 727 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517514 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=C(C(=O)[O-])C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [122, 84, 59, 25, 9, 1, 1, 1, 1, 1, 1, 1, 25, 61, 61, 101, 101, 98, 101, 101, 101, 101, 101, 101, 122, 122, 122, 84, 84, 59, 59, 9, 9, 1, 1, 1, 1, 101, 101, 101] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39]) total number of confs: 624 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517514 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517514 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517514/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517514 Building REAL300004517515 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517515' /scratch/stefan/7774842/working/building/REAL300004517515 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517515 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517515/0 /scratch/stefan/7774842/working/building/REAL300004517515 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 553) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/553 `/scratch/stefan/7774842/working/3D/553' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1CC2(CC(C(=O)[O-])C2)C1) `REAL300004517515.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517515.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517515/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517515 none COCCN(CC1=CC=CC=N1)C(=O)C1CC2(CC(C(=O)[O-])C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [97, 59, 38, 25, 7, 25, 57, 101, 101, 101, 101, 101, 1, 7, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 97, 97, 97, 59, 59, 38, 38, 57, 57, 101, 101, 101, 101, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 22, 23, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 546 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517515 none COCCN(CC1=CC=CC=N1)C(=O)C1CC2(CC(C(=O)[O-])C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [98, 62, 43, 25, 9, 1, 1, 1, 1, 1, 1, 1, 25, 57, 57, 101, 101, 101, 101, 101, 136, 136, 101, 101, 98, 98, 98, 62, 62, 43, 43, 9, 9, 1, 1, 1, 1, 101, 101, 101, 101, 101, 101, 101, 101, 101, 101] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 722 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517515 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517515 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517515/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517515 Building REAL300004517516 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517516' /scratch/stefan/7774842/working/building/REAL300004517516 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517516 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517516/0 /scratch/stefan/7774842/working/building/REAL300004517516 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 554) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/554 `/scratch/stefan/7774842/working/3D/554' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=CC(OC)=CC(C(=O)[O-])=N1) `REAL300004517516.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517516 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC(OC)=CC(C(=O)[O-])=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [105, 73, 57, 25, 8, 25, 53, 95, 95, 95, 95, 95, 1, 8, 1, 1, 1, 1, 3, 1, 1, 1, 2, 2, 1, 105, 105, 105, 73, 73, 57, 57, 53, 53, 95, 95, 95, 95, 1, 3, 3, 3, 1] 201 rigid atoms, others: [38, 42, 12, 14, 15, 16, 17, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 18, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41]) total number of confs: 545 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517516 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC(OC)=CC(C(=O)[O-])=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [130, 90, 64, 30, 8, 1, 1, 1, 1, 1, 1, 1, 30, 75, 75, 95, 95, 95, 121, 95, 95, 95, 95, 95, 95, 130, 130, 130, 90, 90, 64, 64, 8, 8, 1, 1, 1, 1, 95, 121, 121, 121, 95] 201 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 675 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517516 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517516 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517516/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517516 Building REAL300004517517 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517517' /scratch/stefan/7774842/working/building/REAL300004517517 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517517 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517517/0 /scratch/stefan/7774842/working/building/REAL300004517517 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 555) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/555 `/scratch/stefan/7774842/working/3D/555' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=CC=C(C(=O)[O-])N1C) `REAL300004517517.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517517.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517517/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517517 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=C(C(=O)[O-])N1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 180 conformations in input total number of sets (complete confs): 180 using faster count positions algorithm for large data unique positions, atoms: [106, 75, 47, 19, 9, 19, 55, 103, 103, 103, 103, 103, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 106, 106, 106, 75, 75, 47, 47, 55, 55, 103, 103, 103, 103, 1, 1, 2, 2, 2] 180 rigid atoms, others: [36, 37, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40]) total number of confs: 630 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517517 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=C(C(=O)[O-])N1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 180 conformations in input total number of sets (complete confs): 180 using faster count positions algorithm for large data unique positions, atoms: [97, 65, 45, 21, 8, 1, 1, 1, 1, 1, 1, 1, 21, 65, 65, 103, 103, 103, 103, 103, 103, 103, 103, 97, 97, 97, 64, 64, 45, 45, 8, 8, 1, 1, 1, 1, 103, 103, 103, 103, 103] 180 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40]) total number of confs: 527 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517517 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517517 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517517/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517517 Building REAL300004517518 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517518' /scratch/stefan/7774842/working/building/REAL300004517518 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517518 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517518/0 /scratch/stefan/7774842/working/building/REAL300004517518 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 556) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/556 `/scratch/stefan/7774842/working/3D/556' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1(C(=O)[O-])CC=CC1) `REAL300004517518.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517518.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517518/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517518 none COCCN(CC1=CC=CC=N1)C(=O)C1(C(=O)[O-])CC=CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 1, 11, 11, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [24, 17, 11, 7, 3, 7, 14, 21, 21, 21, 21, 21, 1, 3, 1, 1, 3, 3, 1, 1, 1, 1, 24, 24, 24, 17, 17, 11, 11, 14, 14, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1] 33 rigid atoms, others: [35, 36, 37, 38, 39, 40, 12, 14, 15, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 140 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517518 none COCCN(CC1=CC=CC=N1)C(=O)C1(C(=O)[O-])CC=CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 1, 11, 11, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [31, 23, 18, 13, 8, 1, 1, 1, 1, 1, 1, 1, 13, 19, 19, 21, 24, 24, 21, 21, 21, 21, 31, 31, 31, 23, 23, 18, 18, 8, 8, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21] 33 rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40]) total number of confs: 155 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517518 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517518 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517518/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517518 Building REAL300004517519 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517519' /scratch/stefan/7774842/working/building/REAL300004517519 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517519 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517519/0 /scratch/stefan/7774842/working/building/REAL300004517519 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 557) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/557 `/scratch/stefan/7774842/working/3D/557' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=CC=C(CCC(=O)[O-])C=C1) `REAL300004517519.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517519/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517519 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=C(CCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 49, 29, 13, 4, 13, 31, 40, 40, 40, 40, 40, 1, 4, 1, 1, 1, 1, 1, 2, 6, 11, 11, 1, 1, 71, 71, 71, 49, 49, 29, 29, 31, 31, 40, 40, 40, 40, 1, 1, 2, 2, 6, 6, 1, 1] 201 rigid atoms, others: [38, 39, 44, 12, 45, 14, 15, 16, 17, 18, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 379 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517519 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=C(CCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 45, 33, 17, 8, 1, 1, 1, 1, 1, 1, 1, 17, 36, 36, 40, 40, 38, 38, 67, 97, 127, 127, 40, 40, 71, 71, 71, 44, 44, 33, 33, 8, 8, 1, 1, 1, 1, 40, 40, 67, 67, 97, 97, 40, 40] 201 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 740 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517519 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517519 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517519/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517519 Building REAL300004517520 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517520' /scratch/stefan/7774842/working/building/REAL300004517520 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004517520 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517520/0 /scratch/stefan/7774842/working/building/REAL300004517520 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 558) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/558 `/scratch/stefan/7774842/working/3D/558' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=C(C(=O)[O-])C(C)=NN1) `REAL300004517520.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517520/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517520 none COCCN(CC1=CC=CC=N1)C(=O)C1=C(C(=O)[O-])C(C)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 11, 11, 1, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [52, 44, 28, 13, 5, 13, 28, 47, 47, 47, 47, 47, 1, 5, 1, 1, 1, 2, 2, 1, 1, 1, 1, 52, 52, 52, 44, 44, 28, 28, 28, 28, 47, 47, 47, 47, 2, 2, 2, 1] 92 rigid atoms, others: [39, 12, 14, 15, 16, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 327 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517520 none COCCN(CC1=CC=CC=N1)C(=O)C1=C(C(=O)[O-])C(C)=NN1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 11, 11, 1, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 2, 2, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [68, 42, 28, 19, 8, 1, 1, 1, 1, 1, 1, 1, 19, 30, 30, 47, 47, 55, 55, 47, 47, 47, 47, 68, 68, 68, 42, 42, 28, 28, 8, 8, 1, 1, 1, 1, 47, 47, 47, 47] 92 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39]) total number of confs: 335 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517520 /scratch/stefan/7774842/working /scratch/stefan/7774842 mkdir: created directory `1' /scratch/stefan/7774842/working/building/REAL300004517520/1 /scratch/stefan/7774842/working/building/REAL300004517520 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 1 (index: 559) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/559 `/scratch/stefan/7774842/working/3D/559' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=NNC(C)=C1C(=O)[O-]) `REAL300004517520.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004517520.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517520/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517520 none COCCN(CC1=CC=CC=N1)C(=O)C1=NNC(C)=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 8, 8, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [93, 71, 51, 35, 10, 35, 65, 89, 89, 89, 89, 89, 1, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 93, 93, 93, 71, 71, 51, 51, 65, 65, 89, 89, 89, 89, 1, 2, 2, 2] 127 rigid atoms, others: [36, 12, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39]) total number of confs: 513 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517520 none COCCN(CC1=CC=CC=N1)C(=O)C1=NNC(C)=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 8, 8, 1, 5, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 4, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [68, 46, 32, 23, 8, 1, 1, 1, 1, 1, 1, 1, 23, 47, 47, 89, 89, 89, 89, 89, 89, 95, 95, 68, 68, 68, 45, 45, 32, 32, 8, 8, 1, 1, 1, 1, 89, 89, 89, 89] 127 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39]) total number of confs: 386 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517520 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517520 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 1: /scratch/stefan/7774842/working/building/REAL300004517520/1.* 0: /scratch/stefan/7774842/working/building/REAL300004517520/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517520 Building REAL300004517521 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517521' /scratch/stefan/7774842/working/building/REAL300004517521 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517521 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517521/0 /scratch/stefan/7774842/working/building/REAL300004517521 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 560) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/560 `/scratch/stefan/7774842/working/3D/560' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)CC1(CC(=O)[O-])CC1) `REAL300004517521.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517521.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517521/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517521 none COCCN(CC1=CC=CC=N1)C(=O)CC1(CC(=O)[O-])CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [135, 94, 60, 39, 19, 39, 77, 112, 112, 112, 112, 112, 8, 19, 1, 1, 1, 7, 13, 13, 1, 1, 135, 135, 135, 94, 94, 60, 60, 77, 77, 112, 112, 112, 112, 8, 8, 7, 7, 1, 1, 1, 1] 177 rigid atoms, others: [39, 40, 41, 42, 14, 15, 16, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 763 number of broken/clashed sets: 82 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517521 none COCCN(CC1=CC=CC=N1)C(=O)CC1(CC(=O)[O-])CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 177 conformations in input total number of sets (complete confs): 177 using faster count positions algorithm for large data unique positions, atoms: [79, 49, 32, 23, 8, 1, 1, 1, 1, 1, 1, 1, 23, 31, 31, 82, 112, 131, 146, 146, 112, 112, 79, 79, 79, 49, 49, 32, 32, 8, 8, 1, 1, 1, 1, 82, 82, 131, 131, 112, 112, 112, 112] 177 rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 796 number of broken/clashed sets: 82 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517521 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517521 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517521/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517521 Building REAL300004517522 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517522' /scratch/stefan/7774842/working/building/REAL300004517522 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517522 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517522/0 /scratch/stefan/7774842/working/building/REAL300004517522 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 561) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/561 `/scratch/stefan/7774842/working/3D/561' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1CC2(C1)C(C(=O)[O-])C2(F)F) `REAL300004517522.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517522/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517522 none COCCN(CC1=CC=CC=N1)C(=O)C1CC2(C1)C(C(=O)[O-])C2(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [119, 90, 59, 27, 7, 27, 67, 115, 115, 115, 115, 115, 1, 7, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 119, 119, 119, 90, 90, 59, 59, 67, 67, 115, 115, 115, 115, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 703 number of broken/clashed sets: 24 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517522 none COCCN(CC1=CC=CC=N1)C(=O)C1CC2(C1)C(C(=O)[O-])C2(F)F NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [97, 67, 41, 23, 9, 1, 1, 1, 1, 1, 1, 1, 23, 67, 67, 115, 115, 115, 115, 115, 132, 132, 115, 115, 115, 97, 97, 97, 66, 66, 41, 41, 9, 9, 1, 1, 1, 1, 115, 115, 115, 115, 115, 115] 201 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43]) total number of confs: 697 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517522 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517522 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517522/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517522 Building REAL300004517523 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517523' /scratch/stefan/7774842/working/building/REAL300004517523 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517523 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517523/0 /scratch/stefan/7774842/working/building/REAL300004517523 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 562) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/562 `/scratch/stefan/7774842/working/3D/562' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=CSC(C(=O)[O-])=N1) `REAL300004517523.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517523/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517523 none COCCN(CC1=CC=CC=N1)C(=O)C1=CSC(C(=O)[O-])=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 14, 1, 1, 11, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [73, 61, 41, 24, 8, 24, 53, 77, 77, 77, 77, 77, 1, 8, 1, 1, 1, 1, 1, 2, 2, 1, 73, 73, 73, 61, 61, 41, 41, 53, 53, 77, 77, 77, 77, 1] 101 rigid atoms, others: [35, 12, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 469 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517523 none COCCN(CC1=CC=CC=N1)C(=O)C1=CSC(C(=O)[O-])=N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 14, 1, 1, 11, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [67, 49, 33, 21, 8, 1, 1, 1, 1, 1, 1, 1, 21, 49, 49, 77, 77, 77, 77, 77, 77, 77, 67, 67, 67, 48, 48, 33, 33, 8, 8, 1, 1, 1, 1, 77] 101 rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35]) total number of confs: 375 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517523 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517523 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517523/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517523 Building REAL300004517524 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517524' /scratch/stefan/7774842/working/building/REAL300004517524 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517524 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517524/0 /scratch/stefan/7774842/working/building/REAL300004517524 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 563) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/563 `/scratch/stefan/7774842/working/3D/563' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=C(C)SC(C(=O)[O-])=C1) `REAL300004517524.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517524.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517524/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517524 none COCCN(CC1=CC=CC=N1)C(=O)C1=C(C)SC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 5, 14, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [128, 90, 64, 25, 9, 25, 71, 118, 118, 118, 118, 118, 1, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 128, 128, 128, 90, 90, 64, 64, 71, 71, 118, 118, 118, 118, 2, 2, 2, 1] 201 rigid atoms, others: [39, 12, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 754 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517524 none COCCN(CC1=CC=CC=N1)C(=O)C1=C(C)SC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 5, 14, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [118, 66, 46, 22, 8, 1, 1, 1, 1, 1, 1, 1, 22, 68, 68, 118, 118, 118, 118, 118, 118, 118, 118, 118, 118, 118, 66, 66, 46, 46, 8, 8, 1, 1, 1, 1, 118, 118, 118, 118] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39]) total number of confs: 592 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517524 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517524 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517524/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517524 Building REAL300004517525 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517525' /scratch/stefan/7774842/working/building/REAL300004517525 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517525 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517525/0 /scratch/stefan/7774842/working/building/REAL300004517525 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 564) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/564 `/scratch/stefan/7774842/working/3D/564' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=CC2=C(SC(C(=O)[O-])=C2)S1) `REAL300004517525.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517525.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517525/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517525 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC2=C(SC(C(=O)[O-])=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 14, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [129, 95, 64, 28, 10, 28, 62, 118, 118, 118, 118, 118, 1, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 129, 129, 129, 95, 95, 64, 64, 62, 62, 118, 118, 118, 118, 1, 1] 201 rigid atoms, others: [38, 39, 12, 14, 15, 16, 17, 18, 19, 20, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 700 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517525 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC2=C(SC(C(=O)[O-])=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 14, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [85, 55, 39, 19, 8, 1, 1, 1, 1, 1, 1, 1, 19, 65, 65, 118, 118, 117, 118, 118, 118, 118, 118, 118, 118, 85, 85, 85, 54, 54, 39, 39, 8, 8, 1, 1, 1, 1, 118, 118] 201 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39]) total number of confs: 513 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517525 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517525 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517525/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517525 Building REAL300004517526 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517526' /scratch/stefan/7774842/working/building/REAL300004517526 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517526 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517526/0 /scratch/stefan/7774842/working/building/REAL300004517526 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 565) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/565 `/scratch/stefan/7774842/working/3D/565' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=CC(OC)=CC(C(=O)[O-])=C1Cl) `REAL300004517526.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517526.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517526/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517526 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC(OC)=CC(C(=O)[O-])=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [112, 75, 53, 20, 7, 20, 55, 83, 83, 83, 83, 83, 1, 7, 1, 1, 1, 1, 2, 1, 1, 1, 2, 2, 1, 1, 112, 112, 112, 75, 75, 53, 53, 55, 55, 83, 83, 83, 83, 1, 3, 3, 3, 1] 201 rigid atoms, others: [39, 43, 12, 14, 15, 16, 17, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 18, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42]) total number of confs: 611 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517526 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC(OC)=CC(C(=O)[O-])=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [129, 87, 60, 27, 9, 1, 1, 1, 1, 1, 1, 1, 27, 54, 54, 83, 83, 83, 103, 83, 83, 83, 83, 83, 83, 83, 129, 129, 129, 87, 87, 60, 60, 9, 9, 1, 1, 1, 1, 83, 103, 103, 103, 83] 201 rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 10, 11, 38, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43]) total number of confs: 636 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517526 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517526 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517526/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517526 Building REAL300004517527 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517527' /scratch/stefan/7774842/working/building/REAL300004517527 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517527 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517527/0 /scratch/stefan/7774842/working/building/REAL300004517527 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 566) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/566 `/scratch/stefan/7774842/working/3D/566' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=C(F)C=CC(C(=O)[O-])=C1C) `REAL300004517527.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517527.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517527/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517527 none COCCN(CC1=CC=CC=N1)C(=O)C1=C(F)C=CC(C(=O)[O-])=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 15, 1, 1, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [140, 94, 61, 23, 7, 23, 72, 110, 110, 110, 110, 110, 1, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 140, 140, 140, 94, 94, 61, 61, 72, 72, 110, 110, 110, 110, 1, 1, 2, 2, 2] 201 rigid atoms, others: [38, 39, 12, 14, 15, 16, 17, 18, 19, 20, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42]) total number of confs: 774 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517527 none COCCN(CC1=CC=CC=N1)C(=O)C1=C(F)C=CC(C(=O)[O-])=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 15, 1, 1, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [119, 77, 55, 27, 9, 1, 1, 1, 1, 1, 1, 1, 27, 63, 63, 110, 110, 110, 110, 110, 110, 110, 110, 110, 110, 119, 119, 119, 76, 76, 55, 55, 9, 9, 1, 1, 1, 1, 110, 110, 110, 110, 110] 201 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 590 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517527 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517527 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517527/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517527 Building REAL300004517528 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517528' /scratch/stefan/7774842/working/building/REAL300004517528 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517528 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517528/0 /scratch/stefan/7774842/working/building/REAL300004517528 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 567) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/567 `/scratch/stefan/7774842/working/3D/567' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=CC2=C(C(=O)[O-])C=CC=C2S1) `REAL300004517528.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517528.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517528/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517528 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC2=C(C(=O)[O-])C=CC=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 77, 55, 27, 9, 27, 65, 107, 107, 107, 107, 107, 1, 9, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 107, 107, 107, 77, 77, 55, 55, 65, 65, 107, 107, 107, 107, 1, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 631 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517528 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC2=C(C(=O)[O-])C=CC=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 67, 43, 23, 8, 1, 1, 1, 1, 1, 1, 1, 23, 59, 59, 107, 107, 107, 107, 127, 127, 107, 107, 107, 107, 107, 101, 101, 101, 66, 66, 43, 43, 8, 8, 1, 1, 1, 1, 107, 107, 107, 107] 201 rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 10, 11, 38, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42]) total number of confs: 617 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517528 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517528 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517528/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517528 Building REAL300004517529 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517529' /scratch/stefan/7774842/working/building/REAL300004517529 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517529 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517529/0 /scratch/stefan/7774842/working/building/REAL300004517529 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 568) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/568 `/scratch/stefan/7774842/working/3D/568' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)CCC1=CC=CN=C1C(=O)[O-]) `REAL300004517529.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517529.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517529/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517529 none COCCN(CC1=CC=CC=N1)C(=O)CCC1=CC=CN=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 5, 5, 3, 5, 7, 7, 7, 7, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 9, 9, 9, 7, 7, 5, 5, 7, 7, 7, 7, 7, 7, 3, 3, 3, 3, 1, 1, 1] 9 rigid atoms, others: [42, 43, 44, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 50 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517529 none COCCN(CC1=CC=CC=N1)C(=O)CCC1=CC=CN=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 1, 1, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 7, 5, 3, 1, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 9, 9, 9, 9, 7, 7, 3, 3, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7] 9 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 50 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517529 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517529 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517529/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517529 Building REAL300004517530 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517530' /scratch/stefan/7774842/working/building/REAL300004517530 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517530 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517530/0 /scratch/stefan/7774842/working/building/REAL300004517530 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 569) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/569 `/scratch/stefan/7774842/working/3D/569' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C12CC(C(=O)[O-])(C1)CO2) `REAL300004517530.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517530.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517530/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517530 none COCCN(CC1=CC=CC=N1)C(=O)C12CC(C(=O)[O-])(C1)CO2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 11, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 70, 49, 23, 8, 23, 57, 100, 100, 100, 100, 100, 1, 8, 1, 1, 1, 1, 3, 3, 1, 1, 1, 101, 101, 101, 70, 70, 49, 49, 57, 57, 100, 100, 100, 100, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [36, 37, 38, 39, 40, 41, 12, 14, 15, 16, 17, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 563 number of broken/clashed sets: 26 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517530 none COCCN(CC1=CC=CC=N1)C(=O)C12CC(C(=O)[O-])(C1)CO2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 1, 11, 11, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [112, 76, 52, 25, 9, 1, 1, 1, 1, 1, 1, 1, 25, 59, 59, 100, 100, 100, 139, 139, 100, 100, 100, 112, 112, 112, 75, 75, 52, 52, 9, 9, 1, 1, 1, 1, 100, 100, 100, 100, 100, 100] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41]) total number of confs: 718 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517530 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517530 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517530/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517530 Building REAL300004517531 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517531' /scratch/stefan/7774842/working/building/REAL300004517531 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517531 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517531/0 /scratch/stefan/7774842/working/building/REAL300004517531 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 570) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/570 `/scratch/stefan/7774842/working/3D/570' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)/C=C/C1=CC=C(C(=O)[O-])C=C1) `REAL300004517531.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517531/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517531 none COCCN(CC1=CC=CC=N1)C(=O)/C=C/C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [147, 121, 73, 41, 16, 41, 93, 126, 126, 126, 126, 126, 3, 16, 3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 147, 147, 147, 121, 121, 73, 73, 93, 93, 126, 126, 126, 126, 3, 3, 1, 1, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 15, 16, 17, 18, 19, 20, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 886 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517531 none COCCN(CC1=CC=CC=N1)C(=O)/C=C/C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [89, 57, 39, 18, 8, 1, 1, 1, 1, 1, 1, 1, 18, 42, 42, 85, 85, 126, 126, 92, 124, 126, 126, 126, 126, 89, 89, 89, 56, 56, 39, 39, 8, 8, 1, 1, 1, 1, 87, 87, 126, 126, 126, 126] 201 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43]) total number of confs: 746 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517531 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517531 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517531/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517531 Building REAL300004517532 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517532' /scratch/stefan/7774842/working/building/REAL300004517532 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517532 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517532/0 /scratch/stefan/7774842/working/building/REAL300004517532 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 571) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/571 `/scratch/stefan/7774842/working/3D/571' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1(C(=O)[O-])CC2(CCC2)C1) `REAL300004517532.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517532.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517532/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517532 none COCCN(CC1=CC=CC=N1)C(=O)C1(C(=O)[O-])CC2(CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 1, 11, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [12, 8, 7, 6, 3, 6, 11, 20, 20, 20, 20, 20, 1, 3, 1, 1, 3, 3, 1, 1, 1, 1, 1, 1, 12, 12, 12, 8, 8, 7, 7, 11, 11, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 28 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 18, 19, 20, 21, 22, 23, 46, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 16, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 78 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517532 none COCCN(CC1=CC=CC=N1)C(=O)C1(C(=O)[O-])CC2(CCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 1, 11, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 24, 22, 15, 8, 1, 1, 1, 1, 1, 1, 1, 15, 20, 20, 20, 25, 25, 20, 20, 20, 20, 20, 20, 28, 28, 28, 24, 24, 22, 22, 8, 8, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20] 28 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 149 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517532 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517532 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517532/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517532 Building REAL300004517533 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517533' /scratch/stefan/7774842/working/building/REAL300004517533 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517533 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517533/0 /scratch/stefan/7774842/working/building/REAL300004517533 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 572) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/572 `/scratch/stefan/7774842/working/3D/572' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=C(C(=O)[O-])C=NN1C) `REAL300004517533.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517533 none COCCN(CC1=CC=CC=N1)C(=O)C1=C(C(=O)[O-])C=NN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 11, 11, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [130, 93, 61, 21, 7, 21, 61, 105, 105, 105, 105, 105, 1, 7, 1, 1, 1, 3, 3, 1, 1, 1, 1, 130, 130, 130, 93, 93, 61, 61, 61, 61, 105, 105, 105, 105, 1, 2, 2, 2] 201 rigid atoms, others: [36, 12, 14, 15, 16, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39]) total number of confs: 725 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517533 none COCCN(CC1=CC=CC=N1)C(=O)C1=C(C(=O)[O-])C=NN1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 11, 11, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [117, 76, 53, 27, 8, 1, 1, 1, 1, 1, 1, 1, 27, 67, 67, 105, 105, 116, 116, 105, 105, 105, 105, 117, 117, 117, 76, 76, 53, 53, 8, 8, 1, 1, 1, 1, 105, 105, 105, 105] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39]) total number of confs: 625 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517533 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517533 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517533/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517533 Building REAL300004517534 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517534' /scratch/stefan/7774842/working/building/REAL300004517534 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517534 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517534/0 /scratch/stefan/7774842/working/building/REAL300004517534 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 573) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/573 `/scratch/stefan/7774842/working/3D/573' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=CC2=C(N1)C(C(=O)[O-])=CS2) `REAL300004517534.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517534.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517534/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517534 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC2=C(N1)C(C(=O)[O-])=CS2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [140, 104, 75, 37, 11, 37, 82, 139, 139, 139, 139, 139, 1, 11, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 140, 140, 140, 104, 104, 75, 75, 82, 82, 139, 139, 139, 139, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 12, 14, 15, 16, 17, 18, 19, 20, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 804 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517534 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC2=C(N1)C(C(=O)[O-])=CS2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [113, 63, 41, 21, 8, 1, 1, 1, 1, 1, 1, 1, 21, 70, 70, 139, 139, 139, 139, 139, 139, 139, 139, 139, 139, 113, 113, 113, 62, 62, 41, 41, 8, 8, 1, 1, 1, 1, 139, 139, 139] 201 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40]) total number of confs: 582 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517534 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517534 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517534/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517534 Building REAL300004517535 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517535' /scratch/stefan/7774842/working/building/REAL300004517535 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517535 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517535/0 /scratch/stefan/7774842/working/building/REAL300004517535 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 574) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/574 `/scratch/stefan/7774842/working/3D/574' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=CC2=C(C=C(C(=O)[O-])S2)N1) `REAL300004517535.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517535/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517535 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC2=C(C=C(C(=O)[O-])S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [137, 112, 74, 31, 11, 31, 72, 117, 117, 117, 117, 117, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 137, 137, 137, 112, 112, 74, 74, 72, 72, 117, 117, 117, 117, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 790 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517535 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC2=C(C=C(C(=O)[O-])S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 78, 53, 25, 8, 1, 1, 1, 1, 1, 1, 1, 25, 67, 67, 117, 117, 117, 117, 117, 117, 117, 117, 117, 117, 107, 107, 107, 77, 77, 53, 53, 8, 8, 1, 1, 1, 1, 117, 117, 117] 201 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40]) total number of confs: 595 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517535 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517535 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517535/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517535 Building REAL300004517536 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517536' /scratch/stefan/7774842/working/building/REAL300004517536 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517536 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517536/0 /scratch/stefan/7774842/working/building/REAL300004517536 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 575) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/575 `/scratch/stefan/7774842/working/3D/575' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=CC2=C(N1)C(C(=O)[O-])=CO2) `REAL300004517536.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517536.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517536/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517536 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC2=C(N1)C(C(=O)[O-])=CO2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [145, 110, 75, 35, 11, 35, 81, 139, 139, 139, 139, 139, 1, 11, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 145, 145, 145, 110, 110, 75, 75, 81, 81, 139, 139, 139, 139, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 12, 14, 15, 16, 17, 18, 19, 20, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 849 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517536 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC2=C(N1)C(C(=O)[O-])=CO2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 59, 41, 19, 8, 1, 1, 1, 1, 1, 1, 1, 19, 62, 62, 139, 139, 139, 139, 139, 139, 139, 139, 139, 139, 106, 106, 106, 58, 58, 41, 41, 8, 8, 1, 1, 1, 1, 139, 139, 139] 201 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40]) total number of confs: 565 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517536 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517536 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517536/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517536 Building REAL300004517537 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517537' /scratch/stefan/7774842/working/building/REAL300004517537 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517537 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517537/0 /scratch/stefan/7774842/working/building/REAL300004517537 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 576) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/576 `/scratch/stefan/7774842/working/3D/576' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=CC=CC(C(=O)[O-])=C1C) `REAL300004517537.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517537.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517537/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517537 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=CC(C(=O)[O-])=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [131, 91, 59, 23, 7, 23, 67, 104, 104, 104, 104, 104, 1, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 131, 131, 131, 91, 91, 59, 59, 67, 67, 104, 104, 104, 104, 1, 1, 1, 2, 2, 2] 201 rigid atoms, others: [37, 38, 39, 12, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42]) total number of confs: 726 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517537 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=CC(C(=O)[O-])=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [124, 80, 55, 25, 9, 1, 1, 1, 1, 1, 1, 1, 25, 66, 66, 104, 104, 104, 104, 104, 104, 104, 104, 104, 124, 124, 124, 80, 80, 55, 55, 9, 9, 1, 1, 1, 1, 104, 104, 104, 104, 104, 104] 201 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42]) total number of confs: 611 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517537 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517537 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517537/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517537 Building REAL300004517538 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517538' /scratch/stefan/7774842/working/building/REAL300004517538 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517538 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517538/0 /scratch/stefan/7774842/working/building/REAL300004517538 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 577) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/577 `/scratch/stefan/7774842/working/3D/577' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C=CC1=CC=C(C(=O)[O-])N=C1) `REAL300004517538.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517538 none COCCN(CC1=CC=CC=N1)C(=O)C=CC1=CC=C(C(=O)[O-])N=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [156, 134, 84, 59, 23, 59, 102, 130, 130, 130, 130, 130, 5, 23, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 156, 156, 156, 134, 134, 84, 84, 102, 102, 130, 130, 130, 130, 5, 5, 1, 1, 1] 201 rigid atoms, others: [40, 41, 42, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 889 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517538 none COCCN(CC1=CC=CC=N1)C(=O)C=CC1=CC=C(C(=O)[O-])N=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 39, 23, 15, 8, 1, 1, 1, 1, 1, 1, 1, 15, 29, 29, 56, 56, 130, 130, 130, 130, 130, 130, 130, 130, 60, 60, 60, 38, 38, 23, 23, 8, 8, 1, 1, 1, 1, 58, 58, 130, 130, 130] 201 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 453 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517538 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517538 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517538/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517538 Building REAL300004517539 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517539' /scratch/stefan/7774842/working/building/REAL300004517539 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517539 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517539/0 /scratch/stefan/7774842/working/building/REAL300004517539 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 578) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/578 `/scratch/stefan/7774842/working/3D/578' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C=C1CCC1(C(=O)[O-])C(=O)N(CCOC)CC1=CC=CC=N1) `REAL300004517539.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517539.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517539/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517539 none C=C1CCC1(C(=O)[O-])C(=O)N(CCOC)CC1=CC=CC=N1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 11, 1, 11, 8, 5, 5, 12, 5, 5, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 31, 26, 31, 31, 31, 21, 26, 8, 21, 39, 46, 56, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 39, 39, 46, 46, 56, 56, 56, 8, 8, 1, 1, 1, 1] 60 rigid atoms, others: [37, 38, 39, 40, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 245 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517539 none C=C1CCC1(C(=O)[O-])C(=O)N(CCOC)CC1=CC=CC=N1 NO_LONG_NAME dock atom types: ['C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [1, 1, 5, 5, 5, 1, 11, 11, 1, 11, 8, 5, 5, 12, 5, 5, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 60 conformations in input total number of sets (complete confs): 60 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 3, 1, 4, 4, 8, 18, 23, 42, 8, 21, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 1, 18, 18, 23, 23, 42, 42, 42, 21, 21, 31, 31, 31, 31] 60 rigid atoms, others: [0, 1, 2, 3, 4, 5, 8, 22, 23, 24, 25, 26, 27] set([6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517539 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517539 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517539/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517539 Building REAL300004517540 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517540' /scratch/stefan/7774842/working/building/REAL300004517540 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517540 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517540/0 /scratch/stefan/7774842/working/building/REAL300004517540 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 579) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/579 `/scratch/stefan/7774842/working/3D/579' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=CC(C(=O)[O-])=CS1) `REAL300004517540.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517540/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517540 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC(C(=O)[O-])=CS1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [151, 108, 71, 32, 11, 32, 84, 133, 133, 133, 133, 133, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 151, 151, 151, 108, 108, 71, 71, 84, 84, 133, 133, 133, 133, 1, 1] 201 rigid atoms, others: [35, 36, 12, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 867 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517540 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC(C(=O)[O-])=CS1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [98, 50, 34, 21, 8, 1, 1, 1, 1, 1, 1, 1, 21, 61, 61, 133, 133, 133, 133, 133, 133, 133, 98, 98, 98, 50, 49, 34, 34, 8, 8, 1, 1, 1, 1, 133, 133] 201 rigid atoms, others: [32, 33, 34, 5, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36]) total number of confs: 518 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517540 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517540 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517540/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517540 Building REAL300004517541 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517541' /scratch/stefan/7774842/working/building/REAL300004517541 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517541 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517541/0 /scratch/stefan/7774842/working/building/REAL300004517541 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 580) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/580 `/scratch/stefan/7774842/working/3D/580' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)[C@@H]1[C@H]2CC[C@H](O2)[C@@H]1C(=O)[O-]) `REAL300004517541.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517541 none COCCN(CC1=CC=CC=N1)C(=O)[C@@H]1[C@H]2CC[C@H](O2)[C@@H]1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 7, 5, 5, 5, 7, 12, 5, 7, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [32, 22, 14, 9, 3, 9, 18, 26, 26, 26, 26, 26, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 32, 32, 32, 22, 22, 14, 14, 18, 18, 26, 26, 26, 26, 1, 1, 1, 1] 44 rigid atoms, others: [41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 177 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517541 none COCCN(CC1=CC=CC=N1)C(=O)[C@@H]1[C@H]2CC[C@H](O2)[C@@H]1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 7, 5, 5, 5, 7, 12, 5, 7, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [39, 35, 23, 15, 8, 1, 1, 1, 1, 1, 1, 1, 15, 23, 23, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 39, 39, 39, 35, 35, 23, 23, 8, 8, 1, 1, 1, 1, 26, 26, 26, 26] 44 rigid atoms, others: [37, 6, 7, 8, 9, 10, 11, 40, 39, 38, 5] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44]) total number of confs: 198 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517541 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517541 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517541/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517541 Building REAL300004517542 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517542' /scratch/stefan/7774842/working/building/REAL300004517542 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517542 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517542/0 /scratch/stefan/7774842/working/building/REAL300004517542 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 581) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/581 `/scratch/stefan/7774842/working/3D/581' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=CC=CC2=C(C(=O)[O-])C=CC=C12) `REAL300004517542.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517542/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517542 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=CC2=C(C(=O)[O-])C=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [126, 84, 51, 23, 7, 23, 63, 96, 96, 96, 96, 96, 1, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 126, 126, 126, 84, 84, 51, 51, 63, 63, 96, 96, 96, 96, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 662 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517542 none COCCN(CC1=CC=CC=N1)C(=O)C1=CC=CC2=C(C(=O)[O-])C=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 73, 53, 24, 9, 1, 1, 1, 1, 1, 1, 1, 24, 68, 68, 96, 96, 96, 96, 96, 96, 104, 104, 96, 96, 96, 96, 107, 107, 107, 71, 71, 53, 53, 9, 9, 1, 1, 1, 1, 96, 96, 96, 96, 96, 96] 201 rigid atoms, others: [36, 5, 6, 7, 8, 9, 10, 11, 39, 38, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 45]) total number of confs: 560 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517542 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517542 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517542/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517542 Building REAL300004517543 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517543' /scratch/stefan/7774842/working/building/REAL300004517543 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517543 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517543/0 /scratch/stefan/7774842/working/building/REAL300004517543 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 582) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/582 `/scratch/stefan/7774842/working/3D/582' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)[C@@]1(C(C)C)C[C@H]1C(=O)[O-]) `REAL300004517543.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517543.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517543/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517543 none COCCN(CC1=CC=CC=N1)C(=O)[C@@]1(C(C)C)C[C@H]1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [15, 10, 7, 3, 2, 3, 7, 11, 11, 11, 11, 11, 1, 2, 1, 1, 4, 4, 1, 1, 1, 1, 3, 3, 15, 15, 15, 10, 10, 7, 7, 7, 7, 11, 11, 11, 11, 4, 4, 4, 4, 4, 4, 4, 1, 1] 25 rigid atoms, others: [12, 44, 45, 14, 15, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 98 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517543 none COCCN(CC1=CC=CC=N1)C(=O)[C@@]1(C(C)C)C[C@H]1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 5, 5, 7, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [23, 15, 12, 9, 6, 1, 1, 1, 1, 1, 1, 1, 9, 11, 11, 11, 14, 14, 11, 11, 11, 11, 16, 16, 23, 23, 23, 15, 15, 12, 12, 6, 6, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 11, 11] 25 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 124 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517543 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517543 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517543/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517543 Building REAL300004517544 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517544' /scratch/stefan/7774842/working/building/REAL300004517544 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517544 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517544/0 /scratch/stefan/7774842/working/building/REAL300004517544 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 583) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/583 `/scratch/stefan/7774842/working/3D/583' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)CC1=CC=C(C(=O)[O-])C=C1C) `REAL300004517544.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517544.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517544/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517544 none COCCN(CC1=CC=CC=N1)C(=O)CC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [136, 121, 81, 48, 22, 48, 109, 133, 133, 133, 133, 133, 6, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 136, 136, 136, 121, 121, 81, 81, 109, 109, 133, 133, 133, 133, 6, 6, 1, 1, 1, 2, 2, 2] 201 rigid atoms, others: [40, 41, 42, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 43, 44, 45]) total number of confs: 890 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517544 none COCCN(CC1=CC=CC=N1)C(=O)CC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [77, 55, 33, 23, 8, 1, 1, 1, 1, 1, 1, 1, 23, 49, 49, 92, 133, 133, 133, 133, 133, 133, 133, 133, 133, 77, 77, 77, 54, 54, 33, 33, 8, 8, 1, 1, 1, 1, 92, 92, 133, 133, 133, 133, 133, 133] 201 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 616 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517544 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517544 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517544/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517544 Building REAL300004517545 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517545' /scratch/stefan/7774842/working/building/REAL300004517545 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517545 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517545/0 /scratch/stefan/7774842/working/building/REAL300004517545 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 584) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/584 `/scratch/stefan/7774842/working/3D/584' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)CC1=CC(C(=O)[O-])=CS1) `REAL300004517545.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517545.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517545/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517545 none COCCN(CC1=CC=CC=N1)C(=O)CC1=CC(C(=O)[O-])=CS1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [152, 127, 82, 63, 29, 63, 106, 128, 128, 128, 128, 128, 9, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 152, 152, 152, 127, 127, 82, 82, 106, 106, 128, 128, 128, 128, 9, 9, 1, 1] 201 rigid atoms, others: [38, 39, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 814 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517545 none COCCN(CC1=CC=CC=N1)C(=O)CC1=CC(C(=O)[O-])=CS1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [87, 57, 33, 21, 8, 1, 1, 1, 1, 1, 1, 1, 21, 42, 42, 68, 128, 128, 128, 128, 128, 128, 128, 87, 87, 87, 56, 56, 33, 33, 8, 8, 1, 1, 1, 1, 68, 68, 128, 128] 201 rigid atoms, others: [32, 33, 34, 35, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39]) total number of confs: 591 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517545 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517545 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517545/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517545 Building REAL300004517546 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517546' /scratch/stefan/7774842/working/building/REAL300004517546 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517546 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517546/0 /scratch/stefan/7774842/working/building/REAL300004517546 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 585) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/585 `/scratch/stefan/7774842/working/3D/585' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)CC1=CC=C(C(=O)[O-])C(F)=C1) `REAL300004517546.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517546.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517546/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517546 none COCCN(CC1=CC=CC=N1)C(=O)CC1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [142, 132, 84, 58, 19, 58, 100, 124, 124, 124, 124, 124, 7, 19, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 142, 142, 142, 132, 132, 84, 84, 100, 100, 124, 124, 124, 124, 7, 7, 1, 1, 1] 201 rigid atoms, others: [40, 41, 42, 14, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 842 number of broken/clashed sets: 17 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517546 none COCCN(CC1=CC=CC=N1)C(=O)CC1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [62, 47, 27, 19, 8, 1, 1, 1, 1, 1, 1, 1, 19, 31, 31, 63, 124, 124, 124, 124, 129, 129, 124, 124, 124, 62, 62, 62, 46, 46, 27, 27, 8, 8, 1, 1, 1, 1, 63, 63, 124, 124, 124] 201 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42]) total number of confs: 547 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517546 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517546 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517546/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517546 Building REAL300004517547 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517547' /scratch/stefan/7774842/working/building/REAL300004517547 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517547 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517547/0 /scratch/stefan/7774842/working/building/REAL300004517547 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 586) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/586 `/scratch/stefan/7774842/working/3D/586' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)[C@H]1[C@@H](C(=O)[O-])C1(C)C) `REAL300004517547.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517547.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517547/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517547 none COCCN(CC1=CC=CC=N1)C(=O)[C@H]1[C@@H](C(=O)[O-])C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 7, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [50, 31, 21, 10, 3, 10, 26, 46, 46, 46, 46, 46, 1, 3, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 50, 50, 50, 31, 31, 21, 21, 26, 26, 46, 46, 46, 46, 2, 2, 2, 2, 2, 2] 94 rigid atoms, others: [12, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 278 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517547 none COCCN(CC1=CC=CC=N1)C(=O)[C@H]1[C@@H](C(=O)[O-])C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 7, 5, 7, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 94 conformations in input total number of sets (complete confs): 94 using faster count positions algorithm for large data unique positions, atoms: [89, 74, 56, 26, 9, 1, 1, 1, 1, 1, 1, 1, 26, 39, 39, 46, 46, 46, 46, 46, 46, 46, 46, 46, 89, 89, 89, 74, 74, 56, 56, 9, 9, 1, 1, 1, 1, 46, 46, 46, 46, 46, 46] 94 rigid atoms, others: [33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42]) total number of confs: 422 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517547 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517547 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517547/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517547 Building REAL300004517548 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517548' /scratch/stefan/7774842/working/building/REAL300004517548 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517548 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517548/0 /scratch/stefan/7774842/working/building/REAL300004517548 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 587) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/587 `/scratch/stefan/7774842/working/3D/587' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C1=C2CCCCC2=C(C(=O)[O-])S1) `REAL300004517548.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517548.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517548/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517548 none COCCN(CC1=CC=CC=N1)C(=O)C1=C2CCCCC2=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 5, 5, 5, 5, 1, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [108, 72, 53, 23, 9, 23, 61, 93, 93, 93, 93, 93, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 108, 108, 108, 72, 72, 53, 53, 61, 61, 93, 93, 93, 93, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 20, 46, 22, 25, 44, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 601 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517548 none COCCN(CC1=CC=CC=N1)C(=O)C1=C2CCCCC2=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 1, 1, 5, 5, 5, 5, 1, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [98, 63, 46, 23, 8, 1, 1, 1, 1, 1, 1, 1, 23, 63, 63, 93, 93, 93, 93, 93, 93, 93, 93, 115, 115, 93, 98, 98, 98, 63, 63, 46, 46, 8, 8, 1, 1, 1, 1, 93, 93, 93, 93, 93, 93, 93, 93] 201 rigid atoms, others: [35, 36, 5, 6, 7, 8, 9, 10, 11, 38, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 587 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517548 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517548 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517548/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517548 Building REAL300004517549 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517549' /scratch/stefan/7774842/working/building/REAL300004517549 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517549 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517549/0 /scratch/stefan/7774842/working/building/REAL300004517549 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 588) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/588 `/scratch/stefan/7774842/working/3D/588' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCN(CC1=CC=CC=N1)C(=O)C12CCC(C(=O)[O-])(CC1)CC2) `REAL300004517549.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517549.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517549/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517549 none COCCN(CC1=CC=CC=N1)C(=O)C12CCC(C(=O)[O-])(CC1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [41, 27, 21, 9, 4, 9, 11, 13, 13, 13, 13, 13, 1, 4, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 41, 41, 41, 27, 27, 21, 21, 11, 11, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 43 rigid atoms, others: [12, 14, 15, 16, 17, 18, 21, 22, 23, 24, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 165 number of broken/clashed sets: 43 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517549 none COCCN(CC1=CC=CC=N1)C(=O)C12CCC(C(=O)[O-])(CC1)CC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 1, 11, 5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [39, 23, 17, 11, 7, 1, 1, 1, 1, 1, 1, 1, 11, 13, 13, 13, 13, 13, 13, 17, 17, 13, 13, 13, 13, 39, 39, 39, 23, 23, 17, 17, 7, 7, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13] 43 rigid atoms, others: [34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 37] set([0, 1, 2, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 146 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517549 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517549 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517549/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517549 Building REAL300004517550 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517550' /scratch/stefan/7774842/working/building/REAL300004517550 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517550 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517550/0 /scratch/stefan/7774842/working/building/REAL300004517550 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 589) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/589 `/scratch/stefan/7774842/working/3D/589' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(C(=O)C1=CC=CC(OCC(=O)[O-])=C1)C1CCCC1) `REAL300004517550.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517550/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517550 none CC(C)CN(C(=O)C1=CC=CC(OCC(=O)[O-])=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 6, 1, 6, 10, 10, 24, 24, 24, 24, 24, 56, 87, 87, 87, 24, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 24, 24, 24, 87, 87, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1] 89 rigid atoms, others: [4, 38, 39, 40, 41, 42, 43, 44, 45, 46, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 260 number of broken/clashed sets: 20 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517550 none CC(C)CN(C(=O)C1=CC=CC(OCC(=O)[O-])=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 21, 18, 8, 1, 8, 1, 1, 1, 1, 1, 1, 6, 17, 22, 22, 1, 18, 24, 24, 24, 24, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 17, 17, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24] 89 rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 11, 12, 17, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 158 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517550 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517550 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517550/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517550 Building REAL300004517551 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517551' /scratch/stefan/7774842/working/building/REAL300004517551 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517551 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517551/0 /scratch/stefan/7774842/working/building/REAL300004517551 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 590) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/590 `/scratch/stefan/7774842/working/3D/590' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C(=O)N(CC(C)C)C2CCCC2)=CC=C1OCC(=O)[O-]) `REAL300004517551.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517551.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517551/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517551 none CCOC1=CC(C(=O)N(CC(C)C)C2CCCC2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [96, 95, 32, 32, 32, 12, 7, 12, 1, 7, 8, 8, 8, 1, 1, 1, 1, 1, 32, 32, 32, 32, 130, 198, 198, 198, 96, 96, 96, 96, 96, 32, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 198, 198] 201 rigid atoms, others: [48, 45, 49, 8, 41, 42, 43, 44, 13, 14, 15, 16, 17, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 632 number of broken/clashed sets: 30 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517551 none CCOC1=CC(C(=O)N(CC(C)C)C2CCCC2)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 7, 1, 1, 1, 1, 1, 9, 9, 18, 22, 22, 22, 18, 32, 32, 32, 32, 1, 1, 1, 1, 7, 15, 19, 19, 9, 9, 9, 9, 9, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 32, 32, 32, 32, 32, 32, 32, 32, 32, 1, 1, 15, 15] 201 rigid atoms, others: [51, 2, 3, 4, 5, 6, 50, 18, 19, 20, 21, 31] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 52, 53]) total number of confs: 201 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517551 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517551 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517551/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517551 Building REAL300004517552 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517552' /scratch/stefan/7774842/working/building/REAL300004517552 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517552 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517552/0 /scratch/stefan/7774842/working/building/REAL300004517552 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 591) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/591 `/scratch/stefan/7774842/working/3D/591' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(C(=O)CCC1=CC=C(C(=O)[O-])C=C1)C1CCCC1) `REAL300004517552.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517552.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517552/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517552 none CC(C)CN(C(=O)CCC1=CC=C(C(=O)[O-])C=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 5, 1, 5, 9, 9, 20, 21, 23, 23, 21, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 20, 20, 21, 21, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1] 23 rigid atoms, others: [4, 40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 96 number of broken/clashed sets: 19 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517552 none CC(C)CN(C(=O)CCC1=CC=C(C(=O)[O-])C=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 19, 12, 5, 12, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 19, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 5, 5, 4, 4, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23] 23 rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 103 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517552 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517552 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517552/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517552 Building REAL300004517553 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517553' /scratch/stefan/7774842/working/building/REAL300004517553 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517553 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517553/0 /scratch/stefan/7774842/working/building/REAL300004517553 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 592) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/592 `/scratch/stefan/7774842/working/3D/592' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(C(=O)C=CC1=CC=C(C(=O)[O-])C=C1)C1CCCC1) `REAL300004517553.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517553.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517553/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517553 none CC(C)CN(C(=O)C=CC1=CC=C(C(=O)[O-])C=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [9, 8, 9, 5, 1, 5, 9, 9, 30, 30, 33, 33, 30, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 8, 8, 30, 30, 33, 33, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1] 35 rigid atoms, others: [4, 38, 39, 40, 41, 42, 43, 44, 45, 46, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 123 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517553 none CC(C)CN(C(=O)C=CC1=CC=C(C(=O)[O-])C=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 30, 15, 3, 15, 3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 30, 33, 33, 33, 33, 34, 34, 34, 34, 34, 34, 34, 34, 34, 3, 3, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 33, 33, 33] 35 rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 123 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517553 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517553 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517553/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517553 Building REAL300004517554 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517554' /scratch/stefan/7774842/working/building/REAL300004517554 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517554 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517554/0 /scratch/stefan/7774842/working/building/REAL300004517554 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 593) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/593 `/scratch/stefan/7774842/working/3D/593' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(C(=O)CNS(=O)(=O)C1=CC=C(C(=O)[O-])C=C1)C1CCCC1) `REAL300004517554.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517554 none CC(C)CN(C(=O)CNS(=O)(=O)C1=CC=C(C(=O)[O-])C=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 2, 1, 2, 4, 4, 19, 62, 111, 111, 111, 111, 111, 111, 111, 111, 111, 111, 111, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 19, 19, 62, 111, 111, 111, 111, 1, 1, 1, 1, 1, 1, 1, 1, 1] 122 rigid atoms, others: [4, 42, 43, 44, 45, 46, 47, 48, 49, 50, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 434 number of broken/clashed sets: 38 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517554 none CC(C)CN(C(=O)CNS(=O)(=O)C1=CC=C(C(=O)[O-])C=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'S.o2', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 8, 14, 11, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 4, 7, 6, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 122 conformations in input total number of sets (complete confs): 122 using faster count positions algorithm for large data unique positions, atoms: [121, 122, 122, 111, 90, 26, 90, 5, 2, 1, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 111, 111, 111, 111, 111, 122, 122, 122, 122, 122, 122, 122, 122, 122, 26, 26, 5, 1, 1, 1, 1, 111, 111, 111, 111, 111, 111, 111, 111, 111] 122 rigid atoms, others: [38, 39, 40, 9, 12, 13, 14, 15, 16, 17, 18, 19, 20, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 415 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517554 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517554 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517554/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517554 Building REAL300004517555 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517555' /scratch/stefan/7774842/working/building/REAL300004517555 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517555 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517555/0 /scratch/stefan/7774842/working/building/REAL300004517555 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 594) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/594 `/scratch/stefan/7774842/working/3D/594' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(C(=O)C1=CC(C(=O)[O-])=CC([N+](=O)[O-])=C1)C1CCCC1) `REAL300004517555.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517555.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517555/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517555 none CC(C)CN(C(=O)C1=CC(C(=O)[O-])=CC([N+](=O)[O-])=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 7, 1, 7, 12, 12, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 38, 38, 38, 1, 1, 1, 1, 1, 1, 1, 1, 1] 41 rigid atoms, others: [4, 37, 38, 39, 40, 41, 42, 43, 44, 19, 20, 21, 22, 23, 36] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 75 number of broken/clashed sets: 30 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517555 none CC(C)CN(C(=O)C1=CC(C(=O)[O-])=CC([N+](=O)[O-])=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [34, 33, 34, 24, 9, 1, 9, 1, 1, 1, 1, 2, 2, 1, 1, 1, 2, 2, 1, 24, 38, 38, 38, 38, 34, 34, 34, 34, 34, 34, 34, 33, 33, 1, 1, 1, 38, 38, 38, 38, 38, 38, 38, 38, 38] 41 rigid atoms, others: [33, 34, 35, 5, 7, 8, 9, 10, 13, 14, 15, 18] set([0, 1, 2, 3, 4, 6, 11, 12, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 179 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517555 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517555 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517555/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517555 Building REAL300004517556 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517556' /scratch/stefan/7774842/working/building/REAL300004517556 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517556 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517556/0 /scratch/stefan/7774842/working/building/REAL300004517556 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 595) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/595 `/scratch/stefan/7774842/working/3D/595' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(C(=O)C1=CC(C(=O)[O-])=CC([N+](=O)[O-])=C1)C1CCCC1) `REAL300004517556.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517556.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517556/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517556 none CC(C)CN(C(=O)C1=CC(C(=O)[O-])=CC([N+](=O)[O-])=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 7, 1, 7, 12, 12, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 38, 38, 38, 1, 1, 1, 1, 1, 1, 1, 1, 1] 41 rigid atoms, others: [4, 37, 38, 39, 40, 41, 42, 43, 44, 19, 20, 21, 22, 23, 36] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 75 number of broken/clashed sets: 30 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517556 none CC(C)CN(C(=O)C1=CC(C(=O)[O-])=CC([N+](=O)[O-])=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [34, 33, 34, 24, 9, 1, 9, 1, 1, 1, 1, 2, 2, 1, 1, 1, 2, 2, 1, 24, 38, 38, 38, 38, 34, 34, 34, 34, 34, 34, 34, 33, 33, 1, 1, 1, 38, 38, 38, 38, 38, 38, 38, 38, 38] 41 rigid atoms, others: [33, 34, 35, 5, 7, 8, 9, 10, 13, 14, 15, 18] set([0, 1, 2, 3, 4, 6, 11, 12, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 179 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517556 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517556 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517556/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517556 Building REAL300004517557 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517557' /scratch/stefan/7774842/working/building/REAL300004517557 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517557 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517557/0 /scratch/stefan/7774842/working/building/REAL300004517557 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 596) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/596 `/scratch/stefan/7774842/working/3D/596' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=NN1C1=CC=C(C(=O)N(CC(C)C)C2CCCC2)C=C1) `REAL300004517557.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517557 none CC1=C(C(=O)[O-])C=NN1C1=CC=C(C(=O)N(CC(C)C)C2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 8, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 8, 8, 5, 5, 1, 1, 1, 1, 1, 1, 9, 9, 27, 40, 40, 40, 27, 53, 53, 53, 53, 1, 1, 5, 5, 5, 5, 1, 1, 40, 40, 40, 40, 40, 40, 40, 40, 40, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1, 1] 97 rigid atoms, others: [32, 8, 9, 10, 11, 12, 13, 51, 52, 25, 26, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 250 number of broken/clashed sets: 40 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517557 none CC1=C(C(=O)[O-])C=NN1C1=CC=C(C(=O)N(CC(C)C)C2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 8, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 5, 5, 1, 2, 21, 21, 49, 70, 70, 70, 50, 93, 93, 93, 93, 5, 5, 2, 2, 2, 1, 5, 5, 70, 70, 70, 70, 70, 70, 70, 70, 70, 93, 93, 93, 93, 93, 93, 93, 93, 93, 5, 5] 97 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 9, 30] set([4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 420 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517557 none CC1=C(C(=O)[O-])C=NN1C1=CC=C(C(=O)N(CC(C)C)C2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 8, 8, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 97 conformations in input total number of sets (complete confs): 97 using faster count positions algorithm for large data unique positions, atoms: [93, 93, 93, 93, 93, 93, 93, 93, 44, 35, 53, 53, 18, 8, 18, 1, 8, 12, 13, 13, 1, 1, 1, 1, 1, 53, 53, 93, 93, 92, 93, 53, 53, 12, 12, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53] 97 rigid atoms, others: [42, 43, 44, 45, 46, 15, 48, 49, 50, 20, 21, 22, 23, 24, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 275 number of broken/clashed sets: 40 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517557 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517557 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517557/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517557 Building REAL300004517558 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517558' /scratch/stefan/7774842/working/building/REAL300004517558 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517558 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517558/0 /scratch/stefan/7774842/working/building/REAL300004517558 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 597) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/597 `/scratch/stefan/7774842/working/3D/597' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(C(=O)CCC1=CC=CC=C1C(=O)[O-])C1CCCC1) `REAL300004517558.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517558/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517558 none CC(C)CN(C(=O)CCC1=CC=CC=C1C(=O)[O-])C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [9, 9, 9, 7, 1, 7, 12, 12, 43, 45, 51, 51, 51, 51, 51, 51, 51, 51, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 43, 43, 45, 45, 51, 51, 51, 51, 1, 1, 1, 1, 1, 1, 1, 1, 1] 51 rigid atoms, others: [4, 40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 187 number of broken/clashed sets: 43 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517558 none CC(C)CN(C(=O)CCC1=CC=CC=C1C(=O)[O-])C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 45, 38, 17, 6, 17, 4, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 38, 51, 51, 51, 51, 45, 45, 45, 45, 45, 45, 45, 45, 45, 6, 6, 4, 4, 1, 1, 1, 1, 51, 51, 51, 51, 51, 51, 51, 51, 51] 51 rigid atoms, others: [36, 37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 207 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517558 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517558 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517558/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517558 Building REAL300004517559 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517559' /scratch/stefan/7774842/working/building/REAL300004517559 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517559 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517559/0 /scratch/stefan/7774842/working/building/REAL300004517559 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 598) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/598 `/scratch/stefan/7774842/working/3D/598' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)N(CC(C)C)C2CCCC2)=CC(C)=C1OCC(=O)[O-]) `REAL300004517559.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517559/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517559 none CC1=CC(C(=O)N(CC(C)C)C2CCCC2)=CC(C)=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 5, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 10, 6, 10, 1, 6, 8, 8, 8, 1, 1, 1, 1, 1, 28, 28, 28, 10, 10, 30, 75, 78, 78, 28, 28, 28, 28, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 75, 75] 79 rigid atoms, others: [45, 43, 6, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 46, 44] set([0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 348 number of broken/clashed sets: 19 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517559 none CC1=CC(C(=O)N(CC(C)C)C2CCCC2)=CC(C)=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 5, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 79 conformations in input total number of sets (complete confs): 79 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 9, 9, 20, 26, 26, 26, 20, 28, 28, 28, 28, 1, 1, 1, 1, 1, 3, 13, 19, 19, 2, 2, 2, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 28, 28, 28, 28, 28, 28, 28, 28, 28, 1, 2, 2, 2, 13, 13] 79 rigid atoms, others: [0, 1, 2, 3, 4, 47, 16, 17, 18, 19, 20, 28] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50, 51, 52]) total number of confs: 184 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517559 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517559 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517559/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517559 Building REAL300004517560 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517560' /scratch/stefan/7774842/working/building/REAL300004517560 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517560 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517560/0 /scratch/stefan/7774842/working/building/REAL300004517560 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 599) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/599 `/scratch/stefan/7774842/working/3D/599' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(C(=O)CC1=CC=CC(C(=O)[O-])=C1)C1CCCC1) `REAL300004517560.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517560/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517560 none CC(C)CN(C(=O)CC1=CC=CC(C(=O)[O-])=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 7, 1, 7, 14, 14, 31, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 31, 31, 34, 34, 34, 34, 1, 1, 1, 1, 1, 1, 1, 1, 1] 35 rigid atoms, others: [4, 37, 38, 39, 40, 41, 42, 43, 44, 45, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 144 number of broken/clashed sets: 26 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517560 none CC(C)CN(C(=O)CC1=CC=CC(C(=O)[O-])=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 24, 13, 7, 13, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 24, 34, 34, 34, 34, 29, 29, 29, 29, 29, 29, 29, 29, 29, 7, 7, 1, 1, 1, 1, 34, 34, 34, 34, 34, 34, 34, 34, 34] 35 rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 16] set([0, 1, 2, 3, 4, 5, 6, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 144 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517560 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517560 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517560/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517560 Building REAL300004517561 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517561' /scratch/stefan/7774842/working/building/REAL300004517561 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517561 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517561/0 /scratch/stefan/7774842/working/building/REAL300004517561 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 600) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/600 `/scratch/stefan/7774842/working/3D/600' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(C(=O)C1=CC=C(C(=O)[O-])C=C1F)C1CCCC1) `REAL300004517561.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517561 none CC(C)CN(C(=O)C1=CC=C(C(=O)[O-])C=C1F)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 15, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 6, 1, 6, 10, 10, 23, 23, 21, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1] 24 rigid atoms, others: [34, 35, 4, 37, 38, 39, 40, 41, 42, 17, 18, 19, 20, 21, 36] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 66 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517561 none CC(C)CN(C(=O)C1=CC=C(C(=O)[O-])C=C1F)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 15, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 20, 17, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 23, 23, 23, 23, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23] 24 rigid atoms, others: [32, 33, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 77 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517561 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517561 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517561/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517561 Building REAL300004517562 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517562' /scratch/stefan/7774842/working/building/REAL300004517562 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517562 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517562/0 /scratch/stefan/7774842/working/building/REAL300004517562 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 601) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/601 `/scratch/stefan/7774842/working/3D/601' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(C(=O)CC1=CC=C(C(=O)[O-])C=C1)C1CCCC1) `REAL300004517562.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517562.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517562/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517562 none CC(C)CN(C(=O)CC1=CC=C(C(=O)[O-])C=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 3, 1, 3, 7, 7, 22, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 22, 22, 24, 24, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1] 24 rigid atoms, others: [4, 37, 38, 39, 40, 41, 42, 43, 44, 45, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 95 number of broken/clashed sets: 17 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517562 none CC(C)CN(C(=O)CC1=CC=C(C(=O)[O-])C=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 23, 13, 3, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 24, 24, 24, 24, 23, 23, 23, 23, 23, 23, 23, 23, 23, 3, 3, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24] 24 rigid atoms, others: [33, 34, 35, 36, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 72 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517562 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517562 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517562/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517562 Building REAL300004517563 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517563' /scratch/stefan/7774842/working/building/REAL300004517563 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517563 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517563/0 /scratch/stefan/7774842/working/building/REAL300004517563 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 602) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/602 `/scratch/stefan/7774842/working/3D/602' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C(=O)N(CC(C)C)C2CCCC2)=CC=C1C(=O)[O-]) `REAL300004517563.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517563.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517563/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517563 none CC1=NC(C(=O)N(CC(C)C)C2CCCC2)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 46, 46, 25, 9, 25, 1, 9, 13, 13, 13, 1, 1, 1, 1, 1, 46, 46, 46, 46, 49, 49, 46, 46, 46, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 40, 41, 42, 11, 12, 13, 14, 15, 38] set([0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44]) total number of confs: 133 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517563 none CC1=NC(C(=O)N(CC(C)C)C2CCCC2)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 9, 9, 22, 30, 30, 30, 22, 46, 46, 46, 46, 1, 1, 1, 1, 3, 3, 2, 2, 2, 30, 30, 30, 30, 30, 30, 30, 30, 30, 46, 46, 46, 46, 46, 46, 46, 46, 46, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 43, 44, 16, 17, 18, 19] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 184 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517563 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517563 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517563/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517563 Building REAL300004517564 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517564' /scratch/stefan/7774842/working/building/REAL300004517564 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517564 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517564/0 /scratch/stefan/7774842/working/building/REAL300004517564 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 603) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/603 `/scratch/stefan/7774842/working/3D/603' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(C(=O)C1=CC(Br)=CC(C(=O)[O-])=C1)C1CCCC1) `REAL300004517564.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517564.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517564/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517564 none CC(C)CN(C(=O)C1=CC(Br)=CC(C(=O)[O-])=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 17, 1, 1, 1, 11, 11, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [11, 10, 11, 7, 1, 7, 11, 11, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 10, 10, 33, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1] 34 rigid atoms, others: [34, 35, 4, 37, 38, 39, 40, 41, 42, 17, 18, 19, 20, 21, 36] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 79 number of broken/clashed sets: 17 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517564 none CC(C)CN(C(=O)C1=CC(Br)=CC(C(=O)[O-])=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 17, 1, 1, 1, 11, 11, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 23, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 23, 33, 33, 33, 33, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 33, 33, 33, 33, 33, 33, 33, 33, 33] 34 rigid atoms, others: [32, 33, 5, 7, 8, 9, 10, 11, 12, 13, 16, 31] set([0, 1, 2, 3, 4, 6, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 115 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517564 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517564 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517564/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517564 Building REAL300004517565 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517565' /scratch/stefan/7774842/working/building/REAL300004517565 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517565 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517565/0 /scratch/stefan/7774842/working/building/REAL300004517565 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 604) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/604 `/scratch/stefan/7774842/working/3D/604' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(C(=O)C1=CC=CC(CC(=O)[O-])=C1)C1CCCC1) `REAL300004517565.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517565.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517565/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517565 none CC(C)CN(C(=O)C1=CC=CC(CC(=O)[O-])=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [10, 9, 10, 6, 1, 6, 10, 10, 33, 33, 18, 33, 33, 44, 45, 45, 33, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 9, 9, 33, 33, 29, 44, 44, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1] 46 rigid atoms, others: [4, 37, 38, 39, 40, 41, 42, 43, 44, 45, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 206 number of broken/clashed sets: 17 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517565 none CC(C)CN(C(=O)C1=CC=CC(CC(=O)[O-])=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 46 conformations in input total number of sets (complete confs): 46 using default count positions algorithm for smaller data unique positions, atoms: [27, 27, 27, 23, 9, 1, 9, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 23, 33, 33, 33, 33, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 2, 2, 1, 33, 33, 33, 33, 33, 33, 33, 33, 33] 46 rigid atoms, others: [32, 33, 36, 5, 7, 8, 9, 10, 11, 12, 16, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 135 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517565 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517565 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517565/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517565 Building REAL300004517566 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517566' /scratch/stefan/7774842/working/building/REAL300004517566 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517566 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517566/0 /scratch/stefan/7774842/working/building/REAL300004517566 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 605) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/605 `/scratch/stefan/7774842/working/3D/605' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=COC(CC(=O)[O-])=C1C(=O)N(CC(C)C)C1CCCC1) `REAL300004517566.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517566.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517566/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517566 none CC1=COC(CC(=O)[O-])=C1C(=O)N(CC(C)C)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 5, 1, 11, 11, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 17, 17, 17, 8, 5, 8, 1, 5, 7, 7, 7, 1, 1, 1, 1, 1, 14, 14, 14, 14, 17, 17, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1] 17 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 44, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 58 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517566 none CC1=COC(CC(=O)[O-])=C1C(=O)N(CC(C)C)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 5, 1, 11, 11, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 17 conformations in input total number of sets (complete confs): 17 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 7, 7, 12, 13, 13, 13, 12, 14, 14, 14, 14, 2, 2, 2, 1, 3, 3, 13, 13, 13, 13, 13, 13, 13, 13, 13, 14, 14, 14, 14, 14, 14, 14, 14, 14] 17 rigid atoms, others: [0, 1, 2, 3, 4, 5, 9, 10, 25] set([6, 7, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 72 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517566 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517566 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517566/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517566 Building REAL300004517567 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517567' /scratch/stefan/7774842/working/building/REAL300004517567 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517567 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517567/0 /scratch/stefan/7774842/working/building/REAL300004517567 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 606) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/606 `/scratch/stefan/7774842/working/3D/606' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(C(=O)CC1CCC(C(=O)[O-])CC1)C1CCCC1) `REAL300004517567.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517567.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517567/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517567 none CC(C)CN(C(=O)CC1CCC(C(=O)[O-])CC1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 5, 1, 5, 9, 9, 27, 35, 35, 35, 35, 36, 36, 35, 35, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 1, 1, 1, 1, 1, 1] 36 rigid atoms, others: [51, 50, 4, 49, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 137 number of broken/clashed sets: 31 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517567 none CC(C)CN(C(=O)CC1CCC(C(=O)[O-])CC1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [34, 34, 34, 24, 13, 3, 13, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 24, 35, 35, 35, 35, 34, 34, 34, 34, 34, 34, 34, 34, 34, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35, 35, 35, 35] 36 rigid atoms, others: [33, 34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 15, 16, 40, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 176 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517567 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517567 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517567/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517567 Building REAL300004517568 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517568' /scratch/stefan/7774842/working/building/REAL300004517568 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517568 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517568/0 /scratch/stefan/7774842/working/building/REAL300004517568 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 607) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/607 `/scratch/stefan/7774842/working/3D/607' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(C(=O)C1=CC=NC2=C(C(=O)[O-])C=NN21)C1CCCC1) `REAL300004517568.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517568.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517568/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517568 none CC(C)CN(C(=O)C1=CC=NC2=C(C(=O)[O-])C=NN21)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 6, 1, 6, 10, 10, 25, 25, 25, 25, 25, 25, 27, 27, 25, 25, 25, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 25, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1] 28 rigid atoms, others: [4, 37, 38, 39, 40, 41, 42, 43, 44, 19, 20, 21, 22, 23, 36] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 65 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517568 none CC(C)CN(C(=O)C1=CC=NC2=C(C(=O)[O-])C=NN21)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 8, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 18, 8, 1, 8, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 18, 25, 25, 25, 25, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25] 28 rigid atoms, others: [33, 34, 35, 5, 7, 8, 9, 10, 11, 12, 13, 16, 17, 18] set([0, 1, 2, 3, 4, 6, 14, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 107 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517568 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517568 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517568/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517568 Building REAL300004517569 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517569' /scratch/stefan/7774842/working/building/REAL300004517569 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517569 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517569/0 /scratch/stefan/7774842/working/building/REAL300004517569 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 608) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/608 `/scratch/stefan/7774842/working/3D/608' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(C(=O)C1=C(CC(=O)[O-])C2=CC=CC=C2N1)C1CCCC1) `REAL300004517569.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517569.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517569/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517569 none CC(C)CN(C(=O)C1=C(CC(=O)[O-])C2=CC=CC=C2N1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 2, 3, 3, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 4 rigid atoms, others: [4, 41, 42, 43, 44, 45, 46, 47, 48, 49, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 13 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517569 none CC(C)CN(C(=O)C1=C(CC(=O)[O-])C2=CC=CC=C2N1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3] 4 rigid atoms, others: [36, 5, 38, 7, 8, 9, 39, 13, 14, 15, 16, 17, 18, 19, 40, 37] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 16 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517569 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517569 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517569/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517569 Building REAL300004517570 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517570' /scratch/stefan/7774842/working/building/REAL300004517570 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517570 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517570/0 /scratch/stefan/7774842/working/building/REAL300004517570 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 609) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/609 `/scratch/stefan/7774842/working/3D/609' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(C(=O)CC1CCCC2=CC=C(C(=O)[O-])C=C21)C1CCCC1) `REAL300004517570.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517570.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517570/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517570 none CC(C)CN(C(=O)CC1CCCC2=CC=C(C(=O)[O-])C=C21)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 3, 1, 3, 7, 7, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1] 14 rigid atoms, others: [4, 54, 55, 47, 48, 49, 50, 51, 52, 21, 22, 23, 24, 25, 53] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 61 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517570 none CC(C)CN(C(=O)CC1CCCC2=CC=C(C(=O)[O-])C=C21)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 7, 4, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 13, 14, 14, 14, 14, 13, 13, 13, 13, 13, 13, 13, 13, 13, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14] 14 rigid atoms, others: [7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 19, 20, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46] set([0, 1, 2, 3, 4, 5, 6, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 51 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517570 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517570 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517570/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517570 Building REAL300004517571 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517571' /scratch/stefan/7774842/working/building/REAL300004517571 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517571 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517571/0 /scratch/stefan/7774842/working/building/REAL300004517571 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 610) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/610 `/scratch/stefan/7774842/working/3D/610' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(C(=O)C1=CC=C(C=CC(=O)[O-])O1)C1CCCC1) `REAL300004517571.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517571.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517571/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517571 none CC(C)CN(C(=O)C1=CC=C(C=CC(=O)[O-])O1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [16, 16, 16, 8, 1, 8, 24, 24, 77, 77, 77, 77, 166, 166, 166, 166, 77, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 77, 77, 166, 166, 1, 1, 1, 1, 1, 1, 1, 1, 1] 168 rigid atoms, others: [35, 4, 37, 38, 39, 40, 41, 42, 43, 17, 18, 19, 20, 21, 36] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 452 number of broken/clashed sets: 19 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517571 none CC(C)CN(C(=O)C1=CC=C(C=CC(=O)[O-])O1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 52, 40, 11, 1, 11, 1, 1, 1, 1, 1, 11, 11, 30, 30, 1, 40, 77, 77, 77, 77, 52, 52, 52, 52, 52, 52, 52, 52, 52, 1, 1, 11, 11, 77, 77, 77, 77, 77, 77, 77, 77, 77] 168 rigid atoms, others: [32, 5, 7, 8, 9, 10, 11, 16, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 362 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517571 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517571 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517571/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517571 Building REAL300004517572 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517572' /scratch/stefan/7774842/working/building/REAL300004517572 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517572 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517572/0 /scratch/stefan/7774842/working/building/REAL300004517572 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 611) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/611 `/scratch/stefan/7774842/working/3D/611' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(C(=O)C1=CC=C(OCC(=O)[O-])C=C1)C1CCCC1) `REAL300004517572.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517572.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517572/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517572 none CC(C)CN(C(=O)C1=CC=C(OCC(=O)[O-])C=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 8, 6, 1, 6, 10, 10, 14, 14, 10, 10, 45, 88, 91, 91, 14, 14, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 14, 14, 88, 88, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1] 92 rigid atoms, others: [4, 38, 39, 40, 41, 42, 43, 44, 45, 46, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 320 number of broken/clashed sets: 29 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517572 none CC(C)CN(C(=O)C1=CC=C(OCC(=O)[O-])C=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 13, 10, 5, 1, 5, 1, 1, 1, 1, 1, 6, 20, 31, 31, 1, 1, 10, 14, 14, 14, 14, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 20, 20, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14] 92 rigid atoms, others: [32, 33, 36, 5, 7, 8, 9, 10, 11, 16, 17, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 157 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517572 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517572 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517572/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517572 Building REAL300004517573 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517573' /scratch/stefan/7774842/working/building/REAL300004517573 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517573 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517573/0 /scratch/stefan/7774842/working/building/REAL300004517573 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 612) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/612 `/scratch/stefan/7774842/working/3D/612' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(C(=O)C1=CC=C(CC(=O)[O-])C=C1)C1CCCC1) `REAL300004517573.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517573.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517573/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517573 none CC(C)CN(C(=O)C1=CC=C(CC(=O)[O-])C=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 5, 1, 5, 9, 9, 11, 11, 10, 11, 18, 19, 19, 11, 11, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 11, 11, 18, 18, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1] 19 rigid atoms, others: [4, 37, 38, 39, 40, 41, 42, 43, 44, 45, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 87 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517573 none CC(C)CN(C(=O)C1=CC=C(CC(=O)[O-])C=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 8, 4, 1, 4, 1, 1, 1, 1, 1, 2, 6, 6, 1, 1, 8, 11, 11, 11, 11, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 2, 2, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11] 19 rigid atoms, others: [32, 35, 36, 5, 7, 8, 9, 10, 11, 15, 16, 31] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 33, 34, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 53 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517573 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517573 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517573/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517573 Building REAL300004517574 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517574' /scratch/stefan/7774842/working/building/REAL300004517574 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517574 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517574/0 /scratch/stefan/7774842/working/building/REAL300004517574 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 613) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/613 `/scratch/stefan/7774842/working/3D/613' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(C(=O)C1=CC=C(C=CC(=O)[O-])C=C1)C1CCCC1) `REAL300004517574.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517574/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517574 none CC(C)CN(C(=O)C1=CC=C(C=CC(=O)[O-])C=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [10, 9, 10, 6, 1, 6, 10, 10, 17, 17, 10, 13, 35, 35, 35, 35, 17, 17, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 9, 9, 17, 17, 35, 35, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1] 36 rigid atoms, others: [4, 38, 39, 40, 41, 42, 43, 44, 45, 46, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 152 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517574 none CC(C)CN(C(=O)C1=CC=C(C=CC(=O)[O-])C=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [16, 15, 16, 11, 5, 1, 5, 1, 1, 1, 1, 1, 5, 5, 12, 12, 1, 1, 11, 17, 17, 17, 17, 16, 16, 16, 16, 16, 16, 16, 15, 15, 1, 1, 5, 5, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17] 36 rigid atoms, others: [32, 33, 36, 5, 7, 8, 9, 10, 11, 16, 17, 37] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 109 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517574 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517574 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517574/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517574 Building REAL300004517575 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517575' /scratch/stefan/7774842/working/building/REAL300004517575 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517575 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517575/0 /scratch/stefan/7774842/working/building/REAL300004517575 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 614) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/614 `/scratch/stefan/7774842/working/3D/614' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(C(=O)C=CC1=CC(C(=O)[O-])=CO1)C1CCCC1) `REAL300004517575.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517575.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517575/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517575 none CC(C)CN(C(=O)C=CC1=CC(C(=O)[O-])=CO1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [11, 10, 11, 7, 1, 7, 11, 11, 38, 38, 74, 74, 74, 74, 74, 74, 74, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 10, 10, 38, 38, 74, 74, 1, 1, 1, 1, 1, 1, 1, 1, 1] 77 rigid atoms, others: [35, 4, 37, 38, 39, 40, 41, 42, 43, 17, 18, 19, 20, 21, 36] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 172 number of broken/clashed sets: 19 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517575 none CC(C)CN(C(=O)C=CC1=CC(C(=O)[O-])=CO1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 66, 63, 47, 12, 47, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 63, 74, 74, 74, 74, 66, 66, 66, 66, 66, 66, 66, 66, 66, 12, 12, 1, 1, 74, 74, 74, 74, 74, 74, 74, 74, 74] 77 rigid atoms, others: [33, 34, 8, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 223 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517575 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517575 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517575/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517575 Building REAL300004517576 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517576' /scratch/stefan/7774842/working/building/REAL300004517576 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517576 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517576/0 /scratch/stefan/7774842/working/building/REAL300004517576 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 615) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/615 `/scratch/stefan/7774842/working/3D/615' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(C(=O)COCC1=C(C(=O)[O-])N=CO1)C1CCCC1) `REAL300004517576.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517576 none CC(C)CN(C(=O)COCC1=C(C(=O)[O-])N=CO1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 11, 11, 8, 1, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 5, 1, 5, 8, 8, 23, 64, 133, 201, 201, 201, 201, 201, 201, 201, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 23, 23, 133, 133, 201, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [4, 37, 38, 39, 40, 41, 42, 43, 44, 45, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 593 number of broken/clashed sets: 117 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517576 none CC(C)CN(C(=O)COCC1=C(C(=O)[O-])N=CO1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 11, 11, 8, 1, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [193, 193, 193, 178, 139, 62, 139, 28, 6, 1, 1, 1, 1, 2, 2, 1, 1, 1, 178, 201, 201, 201, 201, 193, 193, 193, 193, 193, 193, 193, 193, 193, 62, 62, 6, 6, 1, 201, 201, 201, 201, 201, 201, 201, 201, 201] 201 rigid atoms, others: [36, 9, 10, 11, 12, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 775 number of broken/clashed sets: 117 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517576 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517576 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517576/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517576 Building REAL300004517577 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517577' /scratch/stefan/7774842/working/building/REAL300004517577 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517577 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517577/0 /scratch/stefan/7774842/working/building/REAL300004517577 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 616) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/616 `/scratch/stefan/7774842/working/3D/616' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(C(=O)C=CC1=CC=C(C(=O)[O-])O1)C1CCCC1) `REAL300004517577.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517577 none CC(C)CN(C(=O)C=CC1=CC=C(C(=O)[O-])O1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [11, 10, 11, 8, 1, 8, 17, 17, 52, 52, 72, 72, 72, 72, 72, 72, 72, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 10, 10, 52, 52, 72, 72, 1, 1, 1, 1, 1, 1, 1, 1, 1] 74 rigid atoms, others: [35, 4, 37, 38, 39, 40, 41, 42, 43, 17, 18, 19, 20, 21, 36] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 179 number of broken/clashed sets: 51 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517577 none CC(C)CN(C(=O)C=CC1=CC=C(C(=O)[O-])O1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 74 conformations in input total number of sets (complete confs): 74 using faster count positions algorithm for large data unique positions, atoms: [70, 69, 70, 57, 33, 9, 32, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57, 72, 72, 72, 72, 70, 70, 70, 70, 70, 70, 70, 69, 69, 9, 9, 1, 1, 72, 72, 72, 72, 72, 72, 72, 72, 72] 74 rigid atoms, others: [33, 34, 8, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 287 number of broken/clashed sets: 51 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517577 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517577 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517577/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517577 Building REAL300004517578 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517578' /scratch/stefan/7774842/working/building/REAL300004517578 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517578 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517578/0 /scratch/stefan/7774842/working/building/REAL300004517578 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 617) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/617 `/scratch/stefan/7774842/working/3D/617' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)N(CC(C)C)C2CCCC2)C=C1C(=O)[O-]) `REAL300004517578.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517578/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517578 none CC1=CC=C(C(=O)N(CC(C)C)C2CCCC2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [26, 26, 26, 26, 10, 6, 10, 1, 6, 8, 9, 9, 1, 1, 1, 1, 1, 26, 26, 26, 29, 29, 26, 26, 26, 26, 26, 8, 8, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26] 31 rigid atoms, others: [43, 36, 37, 38, 7, 40, 41, 42, 39, 12, 13, 14, 15, 16, 44] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 10, 11, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45]) total number of confs: 75 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517578 none CC1=CC=C(C(=O)N(CC(C)C)C2CCCC2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 8, 8, 22, 27, 28, 28, 22, 26, 26, 26, 26, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 27, 27, 28, 28, 28, 28, 28, 28, 28, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1] 31 rigid atoms, others: [0, 1, 2, 3, 4, 5, 45, 17, 18, 19, 25, 26] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 117 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517578 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517578 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517578/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517578 Building REAL300004517579 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517579' /scratch/stefan/7774842/working/building/REAL300004517579 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517579 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517579/0 /scratch/stefan/7774842/working/building/REAL300004517579 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 618) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/618 `/scratch/stefan/7774842/working/3D/618' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=C(C(=O)[O-])C=C1C(=O)N(CC(C)C)C1CCCC1) `REAL300004517579.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517579/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517579 none CC1=NC=C(C(=O)[O-])C=C1C(=O)N(CC(C)C)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 4, 7, 1, 4, 5, 5, 5, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 14 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 44, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 35 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517579 none CC1=NC=C(C(=O)[O-])C=C1C(=O)N(CC(C)C)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 12, 13, 13, 13, 12, 14, 14, 14, 14, 2, 2, 2, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13, 14, 14, 14, 14, 14, 14, 14, 14, 14] 14 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 25, 26] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 53 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517579 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517579 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517579/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517579 Building REAL300004517580 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517580' /scratch/stefan/7774842/working/building/REAL300004517580 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517580 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517580/0 /scratch/stefan/7774842/working/building/REAL300004517580 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 619) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/619 `/scratch/stefan/7774842/working/3D/619' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(C(=O)CCCN1C=CC(C(=O)[O-])=N1)C1CCCC1) `REAL300004517580.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517580.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517580/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517580 none CC(C)CN(C(=O)CCCN1C=CC(C(=O)[O-])=N1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 1, 11, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [5, 5, 5, 4, 1, 4, 4, 4, 16, 19, 27, 51, 51, 51, 51, 51, 51, 51, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 16, 16, 20, 20, 27, 26, 51, 51, 1, 1, 1, 1, 1, 1, 1, 1, 1] 51 rigid atoms, others: [4, 40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 168 number of broken/clashed sets: 32 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517580 none CC(C)CN(C(=O)CCCN1C=CC(C(=O)[O-])=N1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 1, 11, 11, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 51 conformations in input total number of sets (complete confs): 51 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 51, 40, 23, 40, 16, 8, 1, 1, 1, 1, 1, 1, 2, 2, 1, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 23, 23, 16, 16, 8, 8, 1, 1, 51, 51, 51, 51, 51, 51, 51, 51, 51] 51 rigid atoms, others: [38, 39, 9, 10, 11, 12, 13, 14, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 196 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517580 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517580 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517580/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517580 Building REAL300004517581 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517581' /scratch/stefan/7774842/working/building/REAL300004517581 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517581 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517581/0 /scratch/stefan/7774842/working/building/REAL300004517581 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 620) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/620 `/scratch/stefan/7774842/working/3D/620' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(C(=O)[C@H]1CC[C@@H](CCC(=O)[O-])O1)C1CCCC1) `REAL300004517581.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517581.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517581/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517581 none CC(C)CN(C(=O)[C@H]1CC[C@@H](CCC(=O)[O-])O1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 5, 5, 1, 11, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 4, 1, 4, 7, 7, 11, 11, 11, 11, 11, 11, 21, 23, 23, 23, 11, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 11, 11, 11, 11, 21, 21, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1] 24 rigid atoms, others: [4, 41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 102 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517581 none CC(C)CN(C(=O)[C@H]1CC[C@@H](CCC(=O)[O-])O1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 5, 5, 1, 11, 11, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 10, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 7, 11, 12, 12, 1, 10, 11, 11, 11, 11, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 7, 7, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 24 rigid atoms, others: [33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 13, 18] set([0, 1, 2, 3, 4, 6, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 87 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517581 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517581 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517581/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517581 Building REAL300004517582 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517582' /scratch/stefan/7774842/working/building/REAL300004517582 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517582 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517582/0 /scratch/stefan/7774842/working/building/REAL300004517582 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 621) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/621 `/scratch/stefan/7774842/working/3D/621' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(C(=O)CC[C@@H]1C[C@H](C(=O)[O-])CO1)C1CCCC1) `REAL300004517582.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517582.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517582/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517582 none CC(C)CN(C(=O)CC[C@@H]1C[C@H](C(=O)[O-])CO1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 7, 1, 11, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [6, 5, 6, 3, 1, 3, 5, 5, 14, 20, 53, 53, 53, 53, 53, 54, 54, 53, 53, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 5, 5, 14, 14, 22, 22, 53, 53, 53, 53, 1, 1, 1, 1, 1, 1, 1, 1, 1] 57 rigid atoms, others: [4, 41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 206 number of broken/clashed sets: 20 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517582 none CC(C)CN(C(=O)CC[C@@H]1C[C@H](C(=O)[O-])CO1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 7, 1, 11, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 56, 51, 40, 16, 40, 9, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 51, 53, 53, 53, 53, 56, 56, 56, 56, 56, 56, 56, 56, 56, 16, 16, 9, 9, 1, 1, 1, 1, 53, 53, 53, 53, 53, 53, 53, 53, 53] 57 rigid atoms, others: [37, 38, 39, 8, 9, 10, 11, 12, 13, 14, 17, 18, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 15, 16, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 223 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517582 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517582 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517582/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517582 Building REAL300004517583 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517583' /scratch/stefan/7774842/working/building/REAL300004517583 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517583 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517583/0 /scratch/stefan/7774842/working/building/REAL300004517583 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 622) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/622 `/scratch/stefan/7774842/working/3D/622' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(C(=O)[C@@H]1C2C=CC(CC2)[C@@H]1C(=O)[O-])C1CCCC1) `REAL300004517583.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517583.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517583/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517583 none CC(C)CN(C(=O)[C@@H]1C2C=CC(CC2)[C@@H]1C(=O)[O-])C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 1, 1, 5, 5, 5, 5, 7, 1, 11, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 2 rigid atoms, others: [4, 42, 43, 44, 45, 46, 47, 48, 49, 50, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 5 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517583 none CC(C)CN(C(=O)[C@@H]1C2C=CC(CC2)[C@@H]1C(=O)[O-])C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 1, 1, 5, 5, 5, 5, 7, 1, 11, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2] 2 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 40, 17, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 9 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517583 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517583 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517583/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517583 Building REAL300004517584 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517584' /scratch/stefan/7774842/working/building/REAL300004517584 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004517584 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517584/0 /scratch/stefan/7774842/working/building/REAL300004517584 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 623) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/623 `/scratch/stefan/7774842/working/3D/623' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(C(=O)C[N@@H+]1CCCC(C(=O)[O-])C1)C1CCCC1) `REAL300004517584.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517584/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517584 none CC(C)CN(C(=O)C[N@@H+]1CCCC(C(=O)[O-])C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 14, 10, 1, 10, 26, 26, 53, 68, 68, 68, 68, 68, 68, 69, 69, 68, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 53, 53, 68, 68, 68, 68, 68, 68, 68, 68, 68, 1, 1, 1, 1, 1, 1, 1, 1, 1] 71 rigid atoms, others: [51, 50, 4, 43, 44, 45, 46, 47, 48, 49, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 270 number of broken/clashed sets: 39 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517584 none CC(C)CN(C(=O)C[N@@H+]1CCCC(C(=O)[O-])C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 49, 35, 13, 5, 13, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 35, 68, 68, 68, 68, 49, 49, 49, 49, 49, 49, 49, 49, 49, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 68, 68, 68, 68, 68, 68, 68, 68, 68] 71 rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 14, 17, 41, 40, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 287 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517584 /scratch/stefan/7774842/working /scratch/stefan/7774842 mkdir: created directory `1' /scratch/stefan/7774842/working/building/REAL300004517584/1 /scratch/stefan/7774842/working/building/REAL300004517584 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 1 (index: 624) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/624 `/scratch/stefan/7774842/working/3D/624' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(C(=O)C[N@H+]1CCCC(C(=O)[O-])C1)C1CCCC1) `REAL300004517584.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004517584.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517584/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517584 none CC(C)CN(C(=O)C[N@H+]1CCCC(C(=O)[O-])C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 6, 1, 6, 10, 10, 18, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 18, 18, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1] 20 rigid atoms, others: [51, 50, 4, 43, 44, 45, 46, 47, 48, 49, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 79 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517584 none CC(C)CN(C(=O)C[N@H+]1CCCC(C(=O)[O-])C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [18, 18, 18, 15, 8, 5, 8, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 15, 20, 20, 20, 20, 18, 18, 18, 18, 18, 18, 18, 18, 18, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20] 20 rigid atoms, others: [34, 35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 14, 17, 41, 40, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 90 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517584 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517584 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 1: /scratch/stefan/7774842/working/building/REAL300004517584/1.* 0: /scratch/stefan/7774842/working/building/REAL300004517584/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517584 Building REAL300004517585 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517585' /scratch/stefan/7774842/working/building/REAL300004517585 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517585 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517585/0 /scratch/stefan/7774842/working/building/REAL300004517585 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 625) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/625 `/scratch/stefan/7774842/working/3D/625' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(C(=O)C1=C(CC(=O)[O-])C2=CC=CC=C2N1)C1CCCC1) `REAL300004517585.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517585.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517585/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517585 none CC(C)CN(C(=O)C1=C(CC(=O)[O-])C2=CC=CC=C2N1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 1, 2, 2, 2, 3, 3, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 4, 4, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 4 rigid atoms, others: [4, 41, 42, 43, 44, 45, 46, 47, 48, 49, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 13 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517585 none CC(C)CN(C(=O)C1=C(CC(=O)[O-])C2=CC=CC=C2N1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3] 4 rigid atoms, others: [36, 5, 38, 7, 8, 9, 39, 13, 14, 15, 16, 17, 18, 19, 40, 37] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 16 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517585 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517585 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517585/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517585 Building REAL300004517586 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517586' /scratch/stefan/7774842/working/building/REAL300004517586 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517586 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517586/0 /scratch/stefan/7774842/working/building/REAL300004517586 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 626) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/626 `/scratch/stefan/7774842/working/3D/626' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(C(=O)CN1C=C(C(=O)[O-])C2=CC=CC=C21)C1CCCC1) `REAL300004517586.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517586.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517586/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517586 none CC(C)CN(C(=O)CN1C=C(C(=O)[O-])C2=CC=CC=C21)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [5, 5, 5, 3, 1, 3, 7, 7, 14, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 14, 14, 18, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1] 18 rigid atoms, others: [4, 41, 42, 43, 44, 45, 46, 47, 48, 49, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 69 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517586 none CC(C)CN(C(=O)CN1C=C(C(=O)[O-])C2=CC=CC=C21)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [17, 17, 17, 17, 12, 8, 12, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 17, 18, 18, 18, 18, 17, 17, 17, 17, 17, 17, 17, 17, 17, 8, 8, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18] 18 rigid atoms, others: [36, 37, 38, 7, 8, 9, 10, 11, 14, 15, 16, 17, 18, 19, 40, 39] set([0, 1, 2, 3, 4, 5, 6, 12, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 67 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517586 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517586 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517586/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517586 Building REAL300004517587 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517587' /scratch/stefan/7774842/working/building/REAL300004517587 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517587 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517587/0 /scratch/stefan/7774842/working/building/REAL300004517587 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 627) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/627 `/scratch/stefan/7774842/working/3D/627' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)[O-])C=C1C(=O)N(CC(C)C)C1CCCC1) `REAL300004517587.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517587.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517587/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517587 none CC1=CC=C(C(=O)[O-])C=C1C(=O)N(CC(C)C)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [33, 33, 33, 33, 33, 33, 33, 33, 33, 19, 10, 19, 1, 10, 14, 14, 14, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1] 34 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 44, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 93 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517587 none CC1=CC=C(C(=O)[O-])C=C1C(=O)N(CC(C)C)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 9, 9, 22, 26, 26, 26, 22, 33, 33, 33, 33, 2, 2, 2, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 26, 26, 33, 33, 33, 33, 33, 33, 33, 33, 33] 34 rigid atoms, others: [0, 1, 2, 3, 4, 5, 8, 9, 10, 25, 26, 27] set([6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 129 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517587 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517587 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517587/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517587 Building REAL300004517588 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517588' /scratch/stefan/7774842/working/building/REAL300004517588 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517588 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517588/0 /scratch/stefan/7774842/working/building/REAL300004517588 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 628) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/628 `/scratch/stefan/7774842/working/3D/628' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=NC=C1C(=O)N(CC(C)C)C1CCCC1) `REAL300004517588.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517588.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517588/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517588 none CC1=C(C(=O)[O-])C=NC=C1C(=O)N(CC(C)C)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 11, 11, 11, 11, 11, 6, 4, 6, 1, 4, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1] 11 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 44, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 29 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517588 none CC1=C(C(=O)[O-])C=NC=C1C(=O)N(CC(C)C)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 5, 5, 11, 11, 11, 11, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11] 11 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 9, 10, 25, 26] set([4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 39 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517588 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517588 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517588/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517588 Building REAL300004517589 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517589' /scratch/stefan/7774842/working/building/REAL300004517589 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517589 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517589/0 /scratch/stefan/7774842/working/building/REAL300004517589 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 629) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/629 `/scratch/stefan/7774842/working/3D/629' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1C(=O)N(CC(C)C)C1CCCC1) `REAL300004517589.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517589.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517589/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517589 none CC1=CC(C(=O)[O-])=CC=C1C(=O)N(CC(C)C)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [26, 26, 26, 25, 25, 26, 26, 26, 26, 18, 9, 18, 1, 9, 11, 11, 11, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1] 27 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 44, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 81 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517589 none CC1=CC(C(=O)[O-])=CC=C1C(=O)N(CC(C)C)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 7, 7, 15, 19, 19, 19, 15, 26, 26, 26, 26, 2, 2, 2, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 26, 26, 26, 26, 26, 26, 26, 26, 26] 27 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 25, 26, 27] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 109 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517589 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517589 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517589/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517589 Building REAL300004517590 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517590' /scratch/stefan/7774842/working/building/REAL300004517590 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517590 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517590/0 /scratch/stefan/7774842/working/building/REAL300004517590 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 630) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/630 `/scratch/stefan/7774842/working/3D/630' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(C(=O)C1=CC=C(C(=O)[O-])C=C1Cl)C1CCCC1) `REAL300004517590.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517590.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517590/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517590 none CC(C)CN(C(=O)C1=CC=C(C(=O)[O-])C=C1Cl)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 5, 1, 5, 9, 9, 15, 15, 13, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1] 15 rigid atoms, others: [34, 35, 4, 37, 38, 39, 40, 41, 42, 17, 18, 19, 20, 21, 36] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 53 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517590 none CC(C)CN(C(=O)C1=CC=C(C(=O)[O-])C=C1Cl)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 15, 15, 15, 15, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15] 15 rigid atoms, others: [32, 33, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 6, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 43 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517590 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517590 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517590/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517590 Building REAL300004517591 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517591' /scratch/stefan/7774842/working/building/REAL300004517591 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517591 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517591/0 /scratch/stefan/7774842/working/building/REAL300004517591 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 631) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/631 `/scratch/stefan/7774842/working/3D/631' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(C(=O)C1CC2(CC(C(=O)[O-])C2)C1)C1CCCC1) `REAL300004517591.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517591.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517591/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517591 none CC(C)CN(C(=O)C1CC2(CC(C(=O)[O-])C2)C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 5, 1, 5, 10, 10, 23, 23, 23, 23, 23, 25, 25, 23, 23, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1] 25 rigid atoms, others: [4, 49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 95 number of broken/clashed sets: 13 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517591 none CC(C)CN(C(=O)C1CC2(CC(C(=O)[O-])C2)C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 16, 7, 1, 7, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 16, 23, 23, 23, 23, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23] 25 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 15, 16, 40, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 89 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517591 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517591 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517591/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517591 Building REAL300004517592 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517592' /scratch/stefan/7774842/working/building/REAL300004517592 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517592 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517592/0 /scratch/stefan/7774842/working/building/REAL300004517592 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 632) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/632 `/scratch/stefan/7774842/working/3D/632' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)[O-])=NC(C(=O)N(CC(C)C)C2CCCC2)=C1) `REAL300004517592.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517592.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517592/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517592 none COC1=CC(C(=O)[O-])=NC(C(=O)N(CC(C)C)C2CCCC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [24, 22, 22, 22, 22, 22, 22, 22, 22, 9, 4, 9, 1, 4, 7, 8, 8, 1, 1, 1, 1, 1, 22, 24, 24, 24, 22, 7, 7, 8, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22] 27 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 44, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45]) total number of confs: 67 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517592 none COC1=CC(C(=O)[O-])=NC(C(=O)N(CC(C)C)C2CCCC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 8, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 8, 8, 18, 22, 23, 23, 18, 22, 22, 22, 22, 1, 3, 3, 3, 1, 22, 22, 23, 23, 23, 23, 23, 23, 23, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1] 27 rigid atoms, others: [1, 2, 3, 4, 5, 8, 9, 10, 45, 22, 26] set([0, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 100 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517592 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517592 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517592/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517592 Building REAL300004517593 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517593' /scratch/stefan/7774842/working/building/REAL300004517593 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517593 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517593/0 /scratch/stefan/7774842/working/building/REAL300004517593 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 633) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/633 `/scratch/stefan/7774842/working/3D/633' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(C(=O)C1=CC=C(CCC(=O)[O-])C=C1)C1CCCC1) `REAL300004517593.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517593.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517593/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517593 none CC(C)CN(C(=O)C1=CC=C(CCC(=O)[O-])C=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 5, 1, 11, 11, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 5, 1, 5, 9, 9, 13, 13, 11, 12, 20, 38, 39, 37, 13, 13, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 13, 13, 20, 20, 38, 38, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1] 41 rigid atoms, others: [4, 40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 175 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517593 none CC(C)CN(C(=O)C1=CC=C(CCC(=O)[O-])C=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 5, 1, 11, 11, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 10, 5, 1, 5, 1, 1, 1, 1, 1, 5, 9, 12, 10, 1, 1, 10, 13, 13, 13, 13, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 5, 5, 9, 9, 1, 1, 13, 13, 13, 13, 13, 13, 13, 13, 13] 41 rigid atoms, others: [32, 33, 5, 38, 7, 8, 9, 10, 11, 16, 17, 39] set([0, 1, 2, 3, 4, 6, 12, 13, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 90 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517593 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517593 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517593/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517593 Building REAL300004517594 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517594' /scratch/stefan/7774842/working/building/REAL300004517594 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517594 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517594/0 /scratch/stefan/7774842/working/building/REAL300004517594 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 634) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/634 `/scratch/stefan/7774842/working/3D/634' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(C(=O)C1CC2(C1)C(C(=O)[O-])C2(F)F)C1CCCC1) `REAL300004517594.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517594.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517594/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517594 none CC(C)CN(C(=O)C1CC2(C1)C(C(=O)[O-])C2(F)F)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 15, 15, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 7, 1, 7, 13, 13, 33, 33, 33, 33, 33, 34, 34, 33, 33, 33, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1] 35 rigid atoms, others: [4, 38, 39, 40, 41, 42, 43, 44, 45, 46, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 106 number of broken/clashed sets: 27 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517594 none CC(C)CN(C(=O)C1CC2(C1)C(C(=O)[O-])C2(F)F)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 15, 15, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 20, 7, 1, 7, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 20, 33, 33, 33, 33, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 33, 33, 33] 35 rigid atoms, others: [32, 33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 12, 15, 16, 17, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 159 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517594 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517594 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517594/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517594 Building REAL300004517595 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517595' /scratch/stefan/7774842/working/building/REAL300004517595 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517595 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517595/0 /scratch/stefan/7774842/working/building/REAL300004517595 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 635) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/635 `/scratch/stefan/7774842/working/3D/635' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)N(CC(C)C)C2CCCC2)C=C(C(=O)[O-])S1) `REAL300004517595.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517595.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517595/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517595 none CC1=C(C(=O)N(CC(C)C)C2CCCC2)C=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 9, 5, 9, 1, 5, 7, 7, 7, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14] 14 rigid atoms, others: [33, 34, 35, 36, 5, 38, 39, 40, 41, 10, 11, 12, 13, 14, 37] set([0, 1, 2, 3, 4, 6, 7, 8, 9, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42]) total number of confs: 40 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517595 none CC1=C(C(=O)N(CC(C)C)C2CCCC2)C=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 5, 5, 11, 11, 11, 11, 11, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 11, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1] 14 rigid atoms, others: [0, 1, 2, 3, 42, 15, 16, 17, 18, 19, 20] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 47 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517595 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517595 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517595/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517595 Building REAL300004517596 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517596' /scratch/stefan/7774842/working/building/REAL300004517596 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517596 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517596/0 /scratch/stefan/7774842/working/building/REAL300004517596 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 636) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/636 `/scratch/stefan/7774842/working/3D/636' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(C(=O)C1=CC2=C(SC(C(=O)[O-])=C2)S1)C1CCCC1) `REAL300004517596.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517596.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517596/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517596 none CC(C)CN(C(=O)C1=CC2=C(SC(C(=O)[O-])=C2)S1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 1, 1, 11, 11, 1, 14, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 10, 1, 10, 23, 23, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [34, 35, 4, 37, 38, 39, 40, 41, 42, 18, 19, 20, 21, 22, 36] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 128 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517596 none CC(C)CN(C(=O)C1=CC2=C(SC(C(=O)[O-])=C2)S1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 14, 1, 1, 11, 11, 1, 14, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 39, 29, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 29, 47, 47, 47, 47, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 47, 47, 47, 47, 47, 47, 47, 47, 47] 50 rigid atoms, others: [32, 33, 5, 7, 8, 9, 10, 11, 12, 13, 16, 17] set([0, 1, 2, 3, 4, 6, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 199 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517596 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517596 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517596/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517596 Building REAL300004517597 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517597' /scratch/stefan/7774842/working/building/REAL300004517597 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517597 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517597/0 /scratch/stefan/7774842/working/building/REAL300004517597 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 637) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/637 `/scratch/stefan/7774842/working/3D/637' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)[O-])=C(Cl)C(C(=O)N(CC(C)C)C2CCCC2)=C1) `REAL300004517597.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517597 none COC1=CC(C(=O)[O-])=C(Cl)C(C(=O)N(CC(C)C)C2CCCC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 16, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [32, 30, 30, 30, 30, 30, 31, 31, 30, 30, 17, 9, 17, 1, 9, 12, 12, 12, 1, 1, 1, 1, 1, 30, 32, 32, 32, 30, 12, 12, 12, 12, 12, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30] 32 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 13, 45, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46]) total number of confs: 92 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517597 none COC1=CC(C(=O)[O-])=C(Cl)C(C(=O)N(CC(C)C)C2CCCC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 1, 16, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 7, 7, 17, 22, 22, 22, 17, 30, 30, 30, 30, 1, 2, 2, 2, 1, 22, 22, 22, 22, 22, 22, 22, 22, 22, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1] 32 rigid atoms, others: [1, 2, 3, 4, 5, 8, 9, 10, 11, 46, 23, 27] set([0, 6, 7, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 123 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517597 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517597 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517597/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517597 Building REAL300004517598 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517598' /scratch/stefan/7774842/working/building/REAL300004517598 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517598 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517598/0 /scratch/stefan/7774842/working/building/REAL300004517598 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 638) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/638 `/scratch/stefan/7774842/working/3D/638' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(C(=O)C1=CC2=C(C(=O)[O-])C=CC=C2S1)C1CCCC1) `REAL300004517598.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517598.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517598/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517598 none CC(C)CN(C(=O)C1=CC2=C(C(=O)[O-])C=CC=C2S1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 14, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 6, 1, 6, 10, 10, 30, 30, 30, 30, 33, 33, 30, 30, 30, 30, 30, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 30, 30, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1] 35 rigid atoms, others: [4, 37, 38, 39, 40, 41, 42, 43, 44, 45, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 81 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517598 none CC(C)CN(C(=O)C1=CC2=C(C(=O)[O-])C=CC=C2S1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 14, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [29, 29, 29, 21, 9, 1, 9, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 21, 30, 30, 30, 30, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 30, 30, 30, 30, 30, 30, 30, 30, 30] 35 rigid atoms, others: [33, 34, 35, 36, 5, 7, 8, 9, 10, 11, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 6, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 139 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517598 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517598 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517598/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517598 Building REAL300004517599 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517599' /scratch/stefan/7774842/working/building/REAL300004517599 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517599 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517599/0 /scratch/stefan/7774842/working/building/REAL300004517599 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 639) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/639 `/scratch/stefan/7774842/working/3D/639' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(C(=O)CCC1=CC=CN=C1C(=O)[O-])C1CCCC1) `REAL300004517599.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517599.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517599/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517599 none CC(C)CN(C(=O)CCC1=CC=CN=C1C(=O)[O-])C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 8, 1, 1, 11, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 6, 1, 6, 10, 10, 20, 23, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 20, 20, 23, 23, 35, 35, 35, 1, 1, 1, 1, 1, 1, 1, 1, 1] 38 rigid atoms, others: [4, 39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 112 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517599 none CC(C)CN(C(=O)CCC1=CC=CN=C1C(=O)[O-])C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 8, 1, 1, 11, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [36, 36, 36, 32, 19, 8, 19, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 32, 35, 35, 35, 35, 36, 36, 36, 36, 36, 36, 36, 36, 36, 8, 8, 6, 6, 1, 1, 1, 35, 35, 35, 35, 35, 35, 35, 35, 35] 38 rigid atoms, others: [36, 37, 38, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 143 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517599 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517599 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517599/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517599 Building REAL300004517600 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517600' /scratch/stefan/7774842/working/building/REAL300004517600 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517600 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517600/0 /scratch/stefan/7774842/working/building/REAL300004517600 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 640) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/640 `/scratch/stefan/7774842/working/3D/640' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(C(=O)/C=C/C1=CC=C(C(=O)[O-])C=C1)C1CCCC1) `REAL300004517600.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517600.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517600/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517600 none CC(C)CN(C(=O)/C=C/C1=CC=C(C(=O)[O-])C=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [15, 14, 15, 8, 1, 8, 24, 24, 72, 72, 75, 75, 74, 75, 75, 75, 75, 75, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 14, 14, 73, 73, 75, 75, 75, 75, 1, 1, 1, 1, 1, 1, 1, 1, 1] 77 rigid atoms, others: [4, 38, 39, 40, 41, 42, 43, 44, 45, 46, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 250 number of broken/clashed sets: 21 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517600 none CC(C)CN(C(=O)/C=C/C1=CC=C(C(=O)[O-])C=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 77 conformations in input total number of sets (complete confs): 77 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 56, 45, 16, 3, 16, 3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 45, 75, 75, 75, 75, 56, 56, 56, 56, 56, 56, 56, 56, 56, 3, 3, 1, 1, 1, 1, 75, 75, 75, 75, 75, 75, 75, 75, 75] 77 rigid atoms, others: [34, 35, 36, 37, 8, 9, 10, 11, 12, 13, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 287 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517600 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517600 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517600/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517600 Building REAL300004517601 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517601' /scratch/stefan/7774842/working/building/REAL300004517601 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517601 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517601/0 /scratch/stefan/7774842/working/building/REAL300004517601 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 641) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/641 `/scratch/stefan/7774842/working/3D/641' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(C(=O)C1=CC2=C(N1)C(C(=O)[O-])=CS2)C1CCCC1) `REAL300004517601.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517601.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517601/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517601 none CC(C)CN(C(=O)C1=CC2=C(N1)C(C(=O)[O-])=CS2)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 14, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 6, 1, 6, 10, 10, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 24, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1] 26 rigid atoms, others: [35, 4, 37, 38, 39, 40, 41, 42, 43, 18, 19, 20, 21, 22, 36] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 63 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517601 none CC(C)CN(C(=O)C1=CC2=C(N1)C(C(=O)[O-])=CS2)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 14, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 20, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 20, 24, 24, 24, 24, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24] 26 rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 11, 12, 13, 16, 17] set([0, 1, 2, 3, 4, 6, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 85 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517601 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517601 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517601/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517601 Building REAL300004517602 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517602' /scratch/stefan/7774842/working/building/REAL300004517602 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517602 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517602/0 /scratch/stefan/7774842/working/building/REAL300004517602 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 642) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/642 `/scratch/stefan/7774842/working/3D/642' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(C(=O)C1=CC2=C(C=C(C(=O)[O-])S2)N1)C1CCCC1) `REAL300004517602.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517602/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517602 none CC(C)CN(C(=O)C1=CC2=C(C=C(C(=O)[O-])S2)N1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 14, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [8, 8, 8, 5, 1, 5, 11, 11, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 27, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1] 27 rigid atoms, others: [35, 4, 37, 38, 39, 40, 41, 42, 43, 18, 19, 20, 21, 22, 36] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 66 number of broken/clashed sets: 13 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517602 none CC(C)CN(C(=O)C1=CC2=C(C=C(C(=O)[O-])S2)N1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 14, 8, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [24, 23, 24, 21, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 27, 27, 27, 27, 24, 24, 24, 24, 24, 24, 24, 23, 23, 1, 1, 1, 27, 27, 27, 27, 27, 27, 27, 27, 27] 27 rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 6, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 97 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517602 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517602 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517602/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517602 Building REAL300004517603 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517603' /scratch/stefan/7774842/working/building/REAL300004517603 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517603 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517603/0 /scratch/stefan/7774842/working/building/REAL300004517603 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 643) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/643 `/scratch/stefan/7774842/working/3D/643' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(C(=O)C1=CC2=C(N1)C(C(=O)[O-])=CO2)C1CCCC1) `REAL300004517603.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517603/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517603 none CC(C)CN(C(=O)C1=CC2=C(N1)C(C(=O)[O-])=CO2)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [9, 8, 9, 6, 1, 6, 10, 10, 25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 8, 8, 25, 25, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1] 28 rigid atoms, others: [35, 4, 37, 38, 39, 40, 41, 42, 43, 18, 19, 20, 21, 22, 36] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 63 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517603 none CC(C)CN(C(=O)C1=CC2=C(N1)C(C(=O)[O-])=CO2)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 23, 19, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 19, 25, 25, 25, 25, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25] 28 rigid atoms, others: [32, 33, 34, 5, 7, 8, 9, 10, 11, 12, 13, 16, 17] set([0, 1, 2, 3, 4, 6, 14, 15, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 99 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517603 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517603 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517603/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517603 Building REAL300004517604 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517604' /scratch/stefan/7774842/working/building/REAL300004517604 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517604 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517604/0 /scratch/stefan/7774842/working/building/REAL300004517604 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 644) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/644 `/scratch/stefan/7774842/working/3D/644' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=CC=C1C(=O)N(CC(C)C)C1CCCC1) `REAL300004517604.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517604 none CC1=C(C(=O)[O-])C=CC=C1C(=O)N(CC(C)C)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 9, 9, 9, 5, 3, 5, 1, 3, 4, 4, 4, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 9 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 44, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 26 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517604 none CC1=C(C(=O)[O-])C=CC=C1C(=O)N(CC(C)C)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 5, 5, 9, 9, 9, 9, 9, 9, 9, 9, 9, 2, 2, 2, 1, 1, 1, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9] 9 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 9, 10, 25, 26, 27] set([4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 35 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517604 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517604 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517604/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517604 Building REAL300004517605 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517605' /scratch/stefan/7774842/working/building/REAL300004517605 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517605 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517605/0 /scratch/stefan/7774842/working/building/REAL300004517605 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 645) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/645 `/scratch/stefan/7774842/working/3D/645' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(C(=O)C=CC1=CC=C(C(=O)[O-])N=C1)C1CCCC1) `REAL300004517605.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517605/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517605 none CC(C)CN(C(=O)C=CC1=CC=C(C(=O)[O-])N=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [11, 10, 11, 7, 1, 7, 12, 12, 45, 45, 80, 80, 80, 80, 80, 80, 80, 80, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 10, 10, 45, 45, 80, 80, 80, 1, 1, 1, 1, 1, 1, 1, 1, 1] 84 rigid atoms, others: [4, 37, 38, 39, 40, 41, 42, 43, 44, 45, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 201 number of broken/clashed sets: 32 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517605 none CC(C)CN(C(=O)C=CC1=CC=C(C(=O)[O-])N=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [67, 67, 67, 63, 32, 5, 32, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 63, 80, 80, 80, 80, 67, 67, 67, 67, 67, 67, 67, 67, 67, 5, 5, 1, 1, 1, 80, 80, 80, 80, 80, 80, 80, 80, 80] 84 rigid atoms, others: [34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 251 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517605 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517605 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517605/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517605 Building REAL300004517606 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517606' /scratch/stefan/7774842/working/building/REAL300004517606 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517606 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517606/0 /scratch/stefan/7774842/working/building/REAL300004517606 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 646) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/646 `/scratch/stefan/7774842/working/3D/646' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(C(=O)[C@@H]1[C@H]2CC[C@H](O2)[C@@H]1C(=O)[O-])C1CCCC1) `REAL300004517606.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517606.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517606/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517606 none CC(C)CN(C(=O)[C@@H]1[C@H]2CC[C@H](O2)[C@@H]1C(=O)[O-])C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 7, 5, 5, 5, 7, 12, 5, 7, 1, 11, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 3, 1, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 4 rigid atoms, others: [4, 39, 40, 41, 42, 43, 44, 45, 46, 47, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 17 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517606 none CC(C)CN(C(=O)[C@@H]1[C@H]2CC[C@H](O2)[C@@H]1C(=O)[O-])C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 7, 5, 5, 5, 7, 12, 5, 7, 1, 11, 11, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4] 4 rigid atoms, others: [35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 37] set([0, 1, 2, 3, 4, 6, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 15 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517606 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517606 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517606/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517606 Building REAL300004517607 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517607' /scratch/stefan/7774842/working/building/REAL300004517607 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517607 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517607/0 /scratch/stefan/7774842/working/building/REAL300004517607 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 647) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/647 `/scratch/stefan/7774842/working/3D/647' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(C(=O)C1=CC=CC2=C(C(=O)[O-])C=CC=C12)C1CCCC1) `REAL300004517607.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517607.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517607/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517607 none CC(C)CN(C(=O)C1=CC=CC2=C(C(=O)[O-])C=CC=C12)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 5, 1, 5, 9, 9, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1] 14 rigid atoms, others: [4, 40, 41, 42, 43, 44, 45, 46, 47, 48, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 41 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517607 none CC(C)CN(C(=O)C1=CC=CC2=C(C(=O)[O-])C=CC=C12)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 11, 11, 5, 1, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 11, 14, 14, 14, 14, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14] 14 rigid atoms, others: [34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 16, 17, 18, 19, 39, 37] set([0, 1, 2, 3, 4, 6, 14, 15, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 45 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517607 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517607 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517607/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517607 Building REAL300004517608 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517608' /scratch/stefan/7774842/working/building/REAL300004517608 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517608 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517608/0 /scratch/stefan/7774842/working/building/REAL300004517608 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 648) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/648 `/scratch/stefan/7774842/working/3D/648' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1CC(=O)N(CC(C)C)C1CCCC1) `REAL300004517608.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517608.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517608/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517608 none CC1=CC(C(=O)[O-])=CC=C1CC(=O)N(CC(C)C)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [22, 22, 22, 16, 20, 22, 22, 22, 22, 16, 7, 3, 7, 1, 3, 4, 4, 4, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 16, 16, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 24 rigid atoms, others: [40, 41, 42, 43, 44, 13, 46, 45, 48, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 113 number of broken/clashed sets: 17 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517608 none CC1=CC(C(=O)[O-])=CC=C1CC(=O)N(CC(C)C)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 15, 15, 22, 24, 24, 24, 22, 22, 22, 22, 22, 2, 2, 2, 1, 1, 1, 6, 6, 24, 24, 24, 24, 24, 24, 24, 24, 24, 22, 22, 22, 22, 22, 22, 22, 22, 22] 24 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 26, 27, 28] set([11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 89 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517608 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517608 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517608/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517608 Building REAL300004517609 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517609' /scratch/stefan/7774842/working/building/REAL300004517609 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517609 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517609/0 /scratch/stefan/7774842/working/building/REAL300004517609 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 649) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/649 `/scratch/stefan/7774842/working/3D/649' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(C(=O)CC1=CC(C(=O)[O-])=CS1)C1CCCC1) `REAL300004517609.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517609 none CC(C)CN(C(=O)CC1=CC(C(=O)[O-])=CS1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 11, 11, 1, 14, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 3, 1, 3, 7, 7, 21, 42, 42, 42, 42, 42, 42, 42, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 21, 21, 42, 42, 1, 1, 1, 1, 1, 1, 1, 1, 1] 42 rigid atoms, others: [34, 35, 4, 37, 38, 39, 40, 41, 42, 16, 17, 18, 19, 20, 36] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 120 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517609 none CC(C)CN(C(=O)CC1=CC(C(=O)[O-])=CS1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 11, 11, 1, 14, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 42 conformations in input total number of sets (complete confs): 42 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 41, 25, 9, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 42, 42, 42, 42, 41, 41, 41, 41, 41, 41, 41, 41, 41, 9, 9, 1, 1, 42, 42, 42, 42, 42, 42, 42, 42, 42] 42 rigid atoms, others: [32, 33, 7, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 132 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517609 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517609 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517609/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517609 Building REAL300004517610 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517610' /scratch/stefan/7774842/working/building/REAL300004517610 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517610 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517610/0 /scratch/stefan/7774842/working/building/REAL300004517610 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 650) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/650 `/scratch/stefan/7774842/working/3D/650' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(C(=O)CC1=CC=C(C(=O)[O-])C(F)=C1)C1CCCC1) `REAL300004517610.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517610 none CC(C)CN(C(=O)CC1=CC=C(C(=O)[O-])C(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 3, 1, 3, 7, 7, 25, 48, 48, 48, 48, 49, 49, 48, 48, 48, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 5, 5, 5, 25, 25, 48, 48, 48, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [4, 37, 38, 39, 40, 41, 42, 43, 44, 45, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 146 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517610 none CC(C)CN(C(=O)CC1=CC=C(C(=O)[O-])C(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 45, 25, 6, 25, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 45, 48, 48, 48, 48, 47, 47, 47, 47, 47, 47, 47, 47, 47, 6, 6, 1, 1, 1, 48, 48, 48, 48, 48, 48, 48, 48, 48] 50 rigid atoms, others: [34, 35, 36, 7, 8, 9, 10, 11, 12, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 163 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517610 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517610 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517610/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517610 Building REAL300004517611 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517611' /scratch/stefan/7774842/working/building/REAL300004517611 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517611 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517611/0 /scratch/stefan/7774842/working/building/REAL300004517611 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 651) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/651 `/scratch/stefan/7774842/working/3D/651' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)CN(C(=O)C1=C2CCCCC2=C(C(=O)[O-])S1)C1CCCC1) `REAL300004517611.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517611.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517611/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517611 none CC(C)CN(C(=O)C1=C2CCCCC2=C(C(=O)[O-])S1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 1, 1, 1, 11, 11, 14, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 14, 10, 1, 10, 22, 22, 56, 56, 56, 56, 56, 56, 56, 56, 58, 58, 56, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 56, 56, 56, 56, 56, 56, 56, 56, 1, 1, 1, 1, 1, 1, 1, 1, 1] 59 rigid atoms, others: [4, 41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 134 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517611 none CC(C)CN(C(=O)C1=C2CCCCC2=C(C(=O)[O-])S1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 8, 1, 11, 1, 1, 5, 5, 5, 5, 1, 1, 1, 11, 11, 14, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 58 conformations in input total number of sets (complete confs): 58 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 34, 25, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 25, 55, 55, 55, 55, 34, 34, 34, 34, 34, 34, 34, 34, 34, 1, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 55, 55, 55, 55, 55, 55] 58 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 13, 14, 15, 40, 18, 39, 37] set([0, 1, 2, 3, 4, 6, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 212 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517611 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517611 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517611/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517611 Building REAL300004517612 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517612' /scratch/stefan/7774842/working/building/REAL300004517612 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517612 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517612/0 /scratch/stefan/7774842/working/building/REAL300004517612 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 652) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/652 `/scratch/stefan/7774842/working/3D/652' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C1) `REAL300004517612.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517612 none O=C([O-])C1=CC=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [98, 94, 98, 94, 98, 98, 94, 41, 94, 9, 1, 1, 1, 1, 1, 1, 1, 1, 41, 57, 57, 57, 57, 98, 98, 98, 98, 9, 9, 1, 1, 1, 1, 57, 57, 57, 57, 57, 57, 57, 57, 57, 98, 98] 106 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 368 number of broken/clashed sets: 17 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517612 none O=C([O-])C1=CC=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 7, 7, 16, 44, 93, 93, 93, 93, 93, 93, 16, 30, 30, 30, 30, 1, 1, 1, 1, 44, 44, 93, 93, 93, 93, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1] 101 rigid atoms, others: [1, 3, 4, 5, 6, 7, 42, 43, 23, 24, 25, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 274 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517612 none O=C([O-])C1=CC=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [28, 21, 28, 21, 28, 28, 21, 8, 21, 1, 8, 24, 57, 57, 57, 57, 57, 57, 1, 1, 1, 1, 1, 28, 28, 28, 28, 24, 24, 57, 57, 57, 57, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28] 106 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 9, 18, 19, 20, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43]) total number of confs: 217 number of broken/clashed sets: 17 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517612 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517612 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517612/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517612 Building REAL300004517613 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517613' /scratch/stefan/7774842/working/building/REAL300004517613 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517613 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517613/0 /scratch/stefan/7774842/working/building/REAL300004517613 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 653) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/653 `/scratch/stefan/7774842/working/3D/653' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=CC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=C1) `REAL300004517613.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517613 none O=C([O-])COC1=CC=CC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [186, 186, 186, 139, 68, 68, 68, 68, 68, 42, 27, 42, 7, 1, 1, 1, 1, 1, 1, 1, 1, 27, 33, 33, 33, 33, 68, 186, 186, 68, 68, 68, 7, 7, 1, 1, 1, 1, 33, 33, 33, 33, 33, 33, 33, 33, 33, 68] 201 rigid atoms, others: [34, 35, 36, 37, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 553 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517613 none O=C([O-])COC1=CC=CC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 19, 29, 6, 1, 1, 1, 1, 1, 1, 1, 7, 7, 14, 30, 68, 68, 68, 68, 68, 68, 14, 21, 21, 21, 21, 1, 19, 19, 1, 1, 1, 30, 30, 68, 68, 68, 68, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 10, 47, 26, 29, 30, 31] set([0, 1, 2, 3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 281 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517613 none O=C([O-])COC1=CC=CC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [93, 82, 93, 48, 21, 21, 21, 21, 21, 12, 5, 12, 1, 5, 16, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 21, 82, 82, 21, 21, 21, 16, 16, 33, 33, 33, 33, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21] 201 rigid atoms, others: [38, 39, 40, 41, 42, 43, 12, 45, 46, 44, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47]) total number of confs: 357 number of broken/clashed sets: 6 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517613 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517613 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517613/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517613 Building REAL300004517614 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517614' /scratch/stefan/7774842/working/building/REAL300004517614 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517614 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517614/0 /scratch/stefan/7774842/working/building/REAL300004517614 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 654) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/654 `/scratch/stefan/7774842/working/3D/654' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=C1) `REAL300004517614.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517614.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517614/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517614 none O=C([O-])C1=CC=CC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [175, 175, 175, 175, 175, 175, 175, 104, 42, 104, 9, 1, 1, 1, 1, 1, 1, 1, 1, 42, 69, 69, 69, 69, 175, 175, 175, 175, 9, 9, 1, 1, 1, 1, 69, 69, 69, 69, 69, 69, 69, 69, 69, 175] 187 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 530 number of broken/clashed sets: 27 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517614 none O=C([O-])C1=CC=CC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 28, 84, 175, 175, 175, 175, 175, 175, 28, 53, 53, 53, 53, 1, 1, 1, 1, 84, 84, 175, 175, 175, 175, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1] 187 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 43, 24, 25, 26, 27] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 536 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517614 none O=C([O-])C1=CC=CC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 53, 53, 53, 53, 22, 9, 22, 1, 9, 28, 69, 69, 69, 69, 69, 69, 1, 1, 1, 1, 1, 53, 53, 53, 53, 28, 28, 69, 69, 69, 69, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53] 187 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 10, 19, 20, 21, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43]) total number of confs: 233 number of broken/clashed sets: 27 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517614 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517614 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517614/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517614 Building REAL300004517615 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517615' /scratch/stefan/7774842/working/building/REAL300004517615 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517615 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517615/0 /scratch/stefan/7774842/working/building/REAL300004517615 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 655) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/655 `/scratch/stefan/7774842/working/3D/655' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)S1) `REAL300004517615.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517615.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517615/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517615 none O=C([O-])C1=CC=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [187, 187, 187, 187, 187, 187, 101, 43, 101, 9, 1, 1, 1, 1, 1, 1, 1, 1, 43, 68, 68, 68, 68, 187, 187, 187, 9, 9, 1, 1, 1, 1, 68, 68, 68, 68, 68, 68, 68, 68, 68] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 539 number of broken/clashed sets: 25 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517615 none O=C([O-])C1=CC=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 11, 11, 30, 90, 187, 187, 187, 187, 187, 187, 30, 53, 53, 53, 53, 1, 1, 1, 90, 90, 187, 187, 187, 187, 53, 53, 53, 53, 53, 53, 53, 53, 53] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 23, 24, 25] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 557 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517615 none O=C([O-])C1=CC=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 53, 53, 53, 20, 9, 20, 1, 9, 27, 68, 68, 68, 68, 68, 68, 1, 1, 1, 1, 1, 53, 53, 53, 27, 27, 68, 68, 68, 68, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 9, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 230 number of broken/clashed sets: 25 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517615 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517615 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517615/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517615 Building REAL300004517616 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517616' /scratch/stefan/7774842/working/building/REAL300004517616 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517616 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517616/0 /scratch/stefan/7774842/working/building/REAL300004517616 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 656) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/656 `/scratch/stefan/7774842/working/3D/656' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=N1) `REAL300004517616.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517616.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517616/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517616 none O=C([O-])C1=CC=CC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [108, 108, 108, 108, 108, 108, 108, 86, 36, 86, 9, 1, 1, 1, 1, 1, 1, 1, 1, 36, 70, 70, 70, 70, 108, 108, 108, 108, 9, 9, 1, 1, 1, 1, 70, 70, 70, 70, 70, 70, 70, 70, 70] 139 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 402 number of broken/clashed sets: 28 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517616 none O=C([O-])C1=CC=CC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 22, 49, 108, 108, 108, 108, 108, 108, 22, 49, 49, 49, 49, 1, 1, 1, 1, 49, 49, 108, 108, 108, 108, 49, 49, 49, 49, 49, 49, 49, 49, 49] 139 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 24, 25, 26, 27] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 342 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517616 none O=C([O-])C1=CC=CC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 49, 49, 49, 49, 49, 28, 9, 28, 1, 9, 28, 70, 70, 70, 70, 70, 70, 1, 1, 1, 1, 1, 49, 49, 49, 49, 28, 28, 70, 70, 70, 70, 1, 1, 1, 1, 1, 1, 1, 1, 1] 139 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 10, 19, 20, 21, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 243 number of broken/clashed sets: 28 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517616 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517616 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517616/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517616 Building REAL300004517617 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517617' /scratch/stefan/7774842/working/building/REAL300004517617 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517617 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517617/0 /scratch/stefan/7774842/working/building/REAL300004517617 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 657) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/657 `/scratch/stefan/7774842/working/3D/657' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(CCC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C1) `REAL300004517617.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517617.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517617/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517617 none O=C([O-])C1=CC=C(CCC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 172 conformations in input total number of sets (complete confs): 172 using faster count positions algorithm for large data unique positions, atoms: [167, 155, 167, 155, 167, 167, 155, 144, 89, 42, 89, 8, 1, 1, 1, 1, 1, 1, 1, 1, 42, 55, 55, 55, 55, 167, 167, 167, 167, 155, 155, 144, 144, 8, 8, 1, 1, 1, 1, 55, 55, 55, 55, 55, 55, 55, 55, 55, 167, 167] 172 rigid atoms, others: [35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 739 number of broken/clashed sets: 46 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517617 none O=C([O-])C1=CC=C(CCC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 170 conformations in input total number of sets (complete confs): 170 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 4, 6, 15, 15, 39, 90, 165, 165, 165, 165, 165, 165, 39, 54, 54, 54, 54, 1, 1, 1, 1, 4, 4, 6, 6, 90, 90, 165, 165, 165, 165, 54, 54, 54, 54, 54, 54, 54, 54, 54, 1, 1] 170 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 48, 49, 25, 26, 27, 28] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 536 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517617 none O=C([O-])C1=CC=C(CCC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 172 conformations in input total number of sets (complete confs): 172 using faster count positions algorithm for large data unique positions, atoms: [56, 52, 56, 52, 56, 56, 52, 47, 17, 7, 17, 1, 7, 20, 55, 55, 55, 55, 55, 55, 1, 1, 1, 1, 1, 56, 56, 56, 56, 52, 52, 47, 47, 20, 20, 55, 55, 55, 55, 1, 1, 1, 1, 1, 1, 1, 1, 1, 56, 56] 172 rigid atoms, others: [43, 39, 40, 41, 42, 11, 44, 45, 46, 47, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 323 number of broken/clashed sets: 46 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517617 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517617 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517617/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517617 Building REAL300004517618 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517618' /scratch/stefan/7774842/working/building/REAL300004517618 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517618 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517618/0 /scratch/stefan/7774842/working/building/REAL300004517618 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 658) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/658 `/scratch/stefan/7774842/working/3D/658' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=CC=N1) `REAL300004517618.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517618.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517618/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517618 none O=C([O-])C1=CC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=CC=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 191 conformations in input total number of sets (complete confs): 191 using faster count positions algorithm for large data unique positions, atoms: [178, 178, 178, 178, 178, 104, 42, 104, 9, 1, 1, 1, 1, 1, 1, 1, 1, 42, 71, 71, 71, 71, 178, 178, 178, 178, 9, 9, 1, 1, 1, 1, 71, 71, 71, 71, 71, 71, 71, 71, 71, 178, 178] 191 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 538 number of broken/clashed sets: 28 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517618 none O=C([O-])C1=CC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=CC=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 191 conformations in input total number of sets (complete confs): 191 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 10, 10, 29, 85, 178, 178, 178, 178, 178, 178, 29, 53, 53, 53, 53, 1, 1, 1, 1, 85, 85, 178, 178, 178, 178, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1, 1] 191 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 41, 42, 22, 23, 24, 25] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 542 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517618 none O=C([O-])C1=CC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=CC=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 191 conformations in input total number of sets (complete confs): 191 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 53, 53, 21, 9, 21, 1, 9, 28, 71, 71, 71, 71, 71, 70, 1, 1, 1, 1, 1, 53, 53, 53, 53, 28, 28, 71, 71, 71, 71, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53] 191 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 8, 17, 18, 19, 20, 21, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42]) total number of confs: 236 number of broken/clashed sets: 28 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517618 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517618 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517618/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517618 Building REAL300004517619 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517619' /scratch/stefan/7774842/working/building/REAL300004517619 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517619 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517619/0 /scratch/stefan/7774842/working/building/REAL300004517619 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 659) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/659 `/scratch/stefan/7774842/working/3D/659' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C1) `REAL300004517619.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517619.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517619/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517619 none O=C([O-])C1=CC=C(C=CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [198, 198, 198, 198, 198, 198, 198, 198, 77, 38, 77, 8, 1, 1, 1, 1, 1, 1, 1, 1, 38, 44, 44, 44, 44, 198, 198, 198, 198, 198, 198, 8, 8, 1, 1, 1, 1, 44, 44, 44, 44, 44, 44, 44, 44, 44, 198, 198] 201 rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 611 number of broken/clashed sets: 32 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517619 none O=C([O-])C1=CC=C(C=CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 199 conformations in input total number of sets (complete confs): 199 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 3, 3, 18, 18, 44, 110, 191, 191, 191, 191, 191, 191, 44, 67, 67, 67, 67, 1, 1, 1, 1, 3, 3, 110, 110, 191, 191, 191, 191, 67, 67, 67, 67, 67, 67, 67, 67, 67, 1, 1] 199 rigid atoms, others: [1, 3, 4, 5, 6, 7, 46, 47, 25, 26, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 643 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517619 none O=C([O-])C1=CC=C(C=CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 46, 58, 58, 46, 46, 13, 5, 13, 1, 5, 18, 44, 44, 44, 44, 44, 44, 1, 1, 1, 1, 1, 58, 58, 58, 58, 46, 46, 18, 18, 44, 44, 44, 44, 1, 1, 1, 1, 1, 1, 1, 1, 1, 58, 58] 201 rigid atoms, others: [43, 37, 38, 39, 40, 41, 42, 11, 44, 45, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 291 number of broken/clashed sets: 32 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517619 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517619 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517619/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517619 Building REAL300004517620 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517620' /scratch/stefan/7774842/working/building/REAL300004517620 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517620 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517620/0 /scratch/stefan/7774842/working/building/REAL300004517620 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 660) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/660 `/scratch/stefan/7774842/working/3D/660' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=CC([N+](=O)[O-])=C1) `REAL300004517620.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517620 none O=C([O-])C1=CC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [186, 186, 186, 186, 186, 74, 36, 74, 9, 1, 1, 1, 1, 1, 1, 1, 1, 36, 53, 53, 53, 53, 186, 186, 186, 186, 186, 186, 186, 9, 9, 1, 1, 1, 1, 53, 53, 53, 53, 53, 53, 53, 53, 53, 186, 186] 201 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 443 number of broken/clashed sets: 22 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517620 none O=C([O-])C1=CC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 10, 10, 34, 95, 186, 186, 186, 186, 186, 186, 34, 53, 53, 53, 53, 1, 1, 1, 2, 2, 1, 1, 95, 95, 186, 186, 186, 186, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 44, 45, 22, 23, 24, 27, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 587 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517620 none O=C([O-])C1=CC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 53, 53, 18, 8, 18, 1, 8, 22, 53, 53, 53, 53, 53, 53, 1, 1, 1, 1, 1, 53, 53, 53, 53, 53, 53, 53, 22, 22, 53, 53, 53, 53, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53] 201 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 42, 43, 17, 18, 19, 20, 21, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45]) total number of confs: 201 number of broken/clashed sets: 22 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517620 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517620 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517620/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517620 Building REAL300004517621 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517621' /scratch/stefan/7774842/working/building/REAL300004517621 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517621 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517621/0 /scratch/stefan/7774842/working/building/REAL300004517621 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 661) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/661 `/scratch/stefan/7774842/working/3D/661' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=CC([N+](=O)[O-])=C1) `REAL300004517621.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517621/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517621 none O=C([O-])C1=CC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [186, 186, 186, 186, 186, 74, 36, 74, 9, 1, 1, 1, 1, 1, 1, 1, 1, 36, 53, 53, 53, 53, 186, 186, 186, 186, 186, 186, 186, 9, 9, 1, 1, 1, 1, 53, 53, 53, 53, 53, 53, 53, 53, 53, 186, 186] 201 rigid atoms, others: [32, 33, 34, 9, 10, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 443 number of broken/clashed sets: 22 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517621 none O=C([O-])C1=CC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 10, 10, 34, 95, 186, 186, 186, 186, 186, 186, 34, 53, 53, 53, 53, 1, 1, 1, 2, 2, 1, 1, 95, 95, 186, 186, 186, 186, 53, 53, 53, 53, 53, 53, 53, 53, 53, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 44, 45, 22, 23, 24, 27, 28] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 587 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517621 none O=C([O-])C1=CC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 53, 53, 53, 18, 8, 18, 1, 8, 22, 53, 53, 53, 53, 53, 53, 1, 1, 1, 1, 1, 53, 53, 53, 53, 53, 53, 53, 22, 22, 53, 53, 53, 53, 1, 1, 1, 1, 1, 1, 1, 1, 1, 53, 53] 201 rigid atoms, others: [35, 36, 37, 38, 39, 8, 41, 42, 43, 17, 18, 19, 20, 21, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45]) total number of confs: 201 number of broken/clashed sets: 22 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517621 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517621 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517621/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517621 Building REAL300004517622 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517622' /scratch/stefan/7774842/working/building/REAL300004517622 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517622 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517622/0 /scratch/stefan/7774842/working/building/REAL300004517622 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 662) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/662 `/scratch/stefan/7774842/working/3D/662' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)O1) `REAL300004517622.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517622.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517622/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517622 none O=C([O-])C1=CC=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [164, 164, 164, 164, 164, 164, 97, 35, 97, 9, 1, 1, 1, 1, 1, 1, 1, 1, 35, 84, 84, 84, 84, 164, 164, 164, 9, 9, 1, 1, 1, 1, 84, 84, 84, 84, 84, 84, 84, 84, 84] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 529 number of broken/clashed sets: 20 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517622 none O=C([O-])C1=CC=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 8, 8, 37, 88, 164, 164, 164, 164, 164, 164, 37, 85, 85, 85, 85, 1, 1, 1, 88, 88, 164, 164, 164, 164, 85, 85, 85, 85, 85, 85, 85, 85, 85] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 23, 24, 25] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 582 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517622 none O=C([O-])C1=CC=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [85, 85, 85, 85, 85, 85, 34, 12, 34, 1, 12, 35, 84, 84, 84, 84, 84, 84, 1, 1, 1, 1, 1, 85, 85, 85, 35, 35, 84, 84, 84, 84, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 9, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 324 number of broken/clashed sets: 20 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517622 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517622 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517622/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517622 Building REAL300004517623 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517623' /scratch/stefan/7774842/working/building/REAL300004517623 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517623 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517623/0 /scratch/stefan/7774842/working/building/REAL300004517623 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 663) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/663 `/scratch/stefan/7774842/working/3D/663' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC=C1CCC(=O)N(CC1=CC=CC(F)=C1)C1CCCC1) `REAL300004517623.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517623.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517623/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517623 none O=C([O-])C1=CC=CC=C1CCC(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 38, 38, 38, 38, 38, 38, 37, 34, 16, 10, 16, 7, 1, 1, 1, 1, 1, 1, 1, 1, 10, 16, 16, 16, 16, 38, 38, 38, 38, 37, 37, 34, 34, 7, 7, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16] 40 rigid atoms, others: [37, 38, 39, 40, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 173 number of broken/clashed sets: 36 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517623 none O=C([O-])C1=CC=CC=C1CCC(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 3, 5, 11, 11, 17, 25, 38, 38, 38, 38, 38, 38, 17, 24, 24, 24, 24, 1, 1, 1, 1, 3, 3, 5, 5, 25, 25, 38, 38, 38, 38, 24, 24, 24, 24, 24, 24, 24, 24, 24] 40 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 27, 28, 29, 30] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 155 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517623 none O=C([O-])C1=CC=CC=C1CCC(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [24, 24, 24, 24, 24, 24, 24, 24, 23, 20, 8, 4, 8, 1, 4, 8, 16, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 24, 24, 24, 24, 23, 23, 20, 20, 8, 8, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1] 40 rigid atoms, others: [41, 42, 43, 44, 13, 46, 45, 48, 49, 22, 23, 24, 25, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 125 number of broken/clashed sets: 36 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517623 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517623 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517623/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517623 Building REAL300004517624 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517624' /scratch/stefan/7774842/working/building/REAL300004517624 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517624 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517624/0 /scratch/stefan/7774842/working/building/REAL300004517624 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 664) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/664 `/scratch/stefan/7774842/working/3D/664' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=CC(C)=C1OCC(=O)[O-]) `REAL300004517624.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517624.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517624/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517624 none CC1=CC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=CC(C)=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 5, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [79, 79, 79, 42, 26, 42, 8, 1, 1, 1, 1, 1, 1, 1, 1, 26, 38, 38, 38, 38, 79, 79, 79, 42, 42, 91, 169, 169, 169, 79, 79, 79, 79, 8, 8, 1, 1, 1, 1, 38, 38, 38, 38, 38, 38, 38, 38, 38, 79, 79, 79, 79, 169, 169] 201 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 880 number of broken/clashed sets: 23 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517624 none CC1=CC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=CC(C)=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 5, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 8, 8, 18, 37, 79, 79, 79, 79, 79, 79, 18, 31, 31, 31, 31, 1, 1, 1, 1, 1, 2, 10, 16, 16, 2, 2, 2, 1, 37, 37, 79, 79, 79, 79, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 2, 2, 2, 10, 10] 201 rigid atoms, others: [0, 1, 2, 3, 4, 32, 48, 20, 21, 22, 23, 24] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51, 52, 53]) total number of confs: 314 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517624 none CC1=CC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=CC(C)=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 5, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 14, 7, 14, 1, 7, 16, 38, 38, 38, 38, 38, 38, 1, 1, 1, 1, 1, 31, 31, 31, 14, 14, 32, 78, 80, 80, 31, 31, 31, 31, 16, 16, 38, 38, 38, 38, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 78, 78] 201 rigid atoms, others: [6, 39, 40, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 47] set([0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52, 53]) total number of confs: 438 number of broken/clashed sets: 23 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517624 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517624 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517624/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517624 Building REAL300004517625 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517625' /scratch/stefan/7774842/working/building/REAL300004517625 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517625 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517625/0 /scratch/stefan/7774842/working/building/REAL300004517625 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 665) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/665 `/scratch/stefan/7774842/working/3D/665' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC(CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=C1) `REAL300004517625.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517625/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517625 none O=C([O-])C1=CC=CC(CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [190, 190, 190, 190, 190, 190, 190, 167, 76, 38, 76, 8, 1, 1, 1, 1, 1, 1, 1, 1, 38, 55, 55, 55, 55, 190, 190, 190, 190, 167, 167, 8, 8, 1, 1, 1, 1, 55, 55, 55, 55, 55, 55, 55, 55, 55, 190] 201 rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 742 number of broken/clashed sets: 80 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517625 none O=C([O-])C1=CC=CC(CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 21, 21, 50, 107, 190, 190, 190, 190, 190, 190, 50, 63, 63, 63, 63, 1, 1, 1, 1, 6, 6, 107, 107, 190, 190, 190, 190, 63, 63, 63, 63, 63, 63, 63, 63, 63, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 46, 25, 26, 27, 28] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 598 number of broken/clashed sets: 80 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517625 none O=C([O-])C1=CC=CC(CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 63, 63, 63, 63, 50, 16, 7, 16, 1, 7, 23, 55, 55, 55, 55, 55, 55, 1, 1, 1, 1, 1, 62, 63, 63, 63, 50, 50, 23, 23, 55, 55, 55, 55, 1, 1, 1, 1, 1, 1, 1, 1, 1, 63] 201 rigid atoms, others: [43, 37, 38, 39, 40, 41, 42, 11, 44, 45, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46]) total number of confs: 312 number of broken/clashed sets: 80 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517625 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517625 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517625/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517625 Building REAL300004517626 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517626' /scratch/stefan/7774842/working/building/REAL300004517626 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517626 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517626/0 /scratch/stefan/7774842/working/building/REAL300004517626 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 666) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/666 `/scratch/stefan/7774842/working/3D/666' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1CCCC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C1) `REAL300004517626.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517626/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517626 none O=C([O-])C1CCCC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [37, 35, 37, 35, 35, 35, 35, 35, 27, 35, 9, 1, 1, 1, 1, 1, 1, 1, 1, 27, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 9, 9, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35] 40 rigid atoms, others: [35, 36, 37, 38, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 146 number of broken/clashed sets: 17 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517626 none O=C([O-])C1CCCC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 7, 14, 35, 35, 35, 35, 35, 35, 7, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 35, 35, 35, 35, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1] 40 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 48, 49, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 94 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517626 none O=C([O-])C1CCCC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [14, 10, 14, 10, 10, 10, 10, 9, 6, 9, 1, 6, 14, 35, 35, 35, 35, 35, 35, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 14, 14, 35, 35, 35, 35, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 40 rigid atoms, others: [39, 40, 41, 10, 43, 44, 45, 46, 47, 19, 20, 21, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 108 number of broken/clashed sets: 17 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517626 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517626 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517626/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517626 Building REAL300004517627 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517627' /scratch/stefan/7774842/working/building/REAL300004517627 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517627 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517627/0 /scratch/stefan/7774842/working/building/REAL300004517627 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 667) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/667 `/scratch/stefan/7774842/working/3D/667' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=N1) `REAL300004517627.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517627.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517627/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517627 none O=C([O-])C1=CC=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [185, 185, 185, 185, 185, 185, 95, 42, 95, 9, 1, 1, 1, 1, 1, 1, 1, 1, 42, 59, 59, 59, 59, 185, 185, 185, 185, 9, 9, 1, 1, 1, 1, 59, 59, 59, 59, 59, 59, 59, 59, 59, 185] 201 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 513 number of broken/clashed sets: 30 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517627 none O=C([O-])C1=CC=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 9, 9, 26, 87, 185, 185, 185, 185, 185, 185, 26, 52, 52, 52, 52, 1, 1, 1, 1, 87, 87, 185, 185, 185, 185, 52, 52, 52, 52, 52, 52, 52, 52, 52, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 42, 23, 24, 25, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 547 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517627 none O=C([O-])C1=CC=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 52, 52, 52, 52, 20, 8, 20, 1, 8, 25, 59, 59, 59, 59, 59, 59, 1, 1, 1, 1, 1, 52, 52, 52, 52, 25, 25, 59, 59, 59, 59, 1, 1, 1, 1, 1, 1, 1, 1, 1, 52] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 9, 18, 19, 20, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42]) total number of confs: 216 number of broken/clashed sets: 30 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517627 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517627 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517627/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517627 Building REAL300004517628 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517628' /scratch/stefan/7774842/working/building/REAL300004517628 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517628 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517628/0 /scratch/stefan/7774842/working/building/REAL300004517628 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 668) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/668 `/scratch/stefan/7774842/working/3D/668' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)N=C1) `REAL300004517628.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517628/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517628 none O=C([O-])C1=CC=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)N=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [146, 146, 146, 146, 146, 146, 92, 43, 92, 9, 1, 1, 1, 1, 1, 1, 1, 1, 43, 66, 66, 66, 66, 146, 146, 146, 146, 9, 9, 1, 1, 1, 1, 66, 66, 66, 66, 66, 66, 66, 66, 66, 146] 159 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 450 number of broken/clashed sets: 19 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517628 none O=C([O-])C1=CC=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)N=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 29, 75, 146, 146, 146, 146, 146, 146, 29, 47, 47, 47, 47, 1, 1, 1, 1, 75, 75, 146, 146, 146, 146, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1] 159 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 42, 23, 24, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 445 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517628 none O=C([O-])C1=CC=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)N=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 47, 47, 47, 47, 19, 9, 19, 1, 9, 25, 66, 66, 66, 66, 66, 66, 1, 1, 1, 1, 1, 47, 47, 47, 47, 25, 25, 66, 66, 66, 66, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47] 159 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 9, 18, 19, 20, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42]) total number of confs: 210 number of broken/clashed sets: 19 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517628 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517628 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517628/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517628 Building REAL300004517629 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517629' /scratch/stefan/7774842/working/building/REAL300004517629 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517629 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517629/0 /scratch/stefan/7774842/working/building/REAL300004517629 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 669) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/669 `/scratch/stefan/7774842/working/3D/669' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CC(=O)[O-])CC(=O)N(CC1=CC=CC(F)=C1)C1CCCC1) `REAL300004517629.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517629/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517629 none CC(C)(CC(=O)[O-])CC(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [22, 15, 22, 22, 25, 28, 28, 12, 5, 12, 1, 5, 15, 39, 39, 39, 39, 39, 39, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 25, 25, 15, 15, 15, 15, 39, 39, 39, 39, 1, 1, 1, 1, 1, 1, 1, 1, 1] 82 rigid atoms, others: [40, 41, 10, 43, 44, 45, 46, 47, 48, 19, 20, 21, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 191 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517629 none CC(C)(CC(=O)[O-])CC(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [80, 66, 80, 80, 80, 80, 80, 54, 35, 54, 8, 1, 1, 1, 1, 1, 1, 1, 1, 35, 39, 39, 39, 39, 80, 80, 80, 80, 80, 80, 80, 80, 66, 66, 8, 8, 1, 1, 1, 1, 39, 39, 39, 39, 39, 39, 39, 39, 39] 82 rigid atoms, others: [36, 37, 38, 39, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 333 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517629 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517629 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517629/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517629 Building REAL300004517630 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517630' /scratch/stefan/7774842/working/building/REAL300004517630 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517630 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517630/0 /scratch/stefan/7774842/working/building/REAL300004517630 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 670) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/670 `/scratch/stefan/7774842/working/3D/670' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C(F)=C1) `REAL300004517630.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517630/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517630 none O=C([O-])C1=CC=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [156, 156, 156, 151, 156, 156, 83, 34, 83, 8, 1, 1, 1, 1, 1, 1, 1, 1, 34, 66, 66, 66, 66, 156, 156, 156, 156, 156, 8, 8, 1, 1, 1, 1, 66, 66, 66, 66, 66, 66, 66, 66, 66, 156] 201 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 510 number of broken/clashed sets: 43 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517630 none O=C([O-])C1=CC=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 28, 72, 156, 156, 156, 156, 156, 156, 28, 61, 61, 61, 61, 1, 1, 1, 1, 1, 72, 72, 156, 156, 156, 156, 61, 61, 61, 61, 61, 61, 61, 61, 61, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 43, 23, 24, 25, 26, 27] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 494 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517630 none O=C([O-])C1=CC=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C(F)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 61, 48, 61, 61, 28, 10, 28, 1, 10, 26, 66, 66, 66, 66, 66, 66, 1, 1, 1, 1, 1, 61, 61, 61, 61, 61, 26, 26, 66, 66, 66, 66, 1, 1, 1, 1, 1, 1, 1, 1, 1, 61] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 9, 42, 18, 19, 20, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43]) total number of confs: 304 number of broken/clashed sets: 43 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517630 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517630 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517630/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517630 Building REAL300004517631 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517631' /scratch/stefan/7774842/working/building/REAL300004517631 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517631 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517631/0 /scratch/stefan/7774842/working/building/REAL300004517631 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 671) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/671 `/scratch/stefan/7774842/working/3D/671' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=N1) `REAL300004517631.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517631.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517631/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517631 none O=C([O-])C1=CN=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [139, 139, 139, 139, 139, 139, 91, 43, 91, 9, 1, 1, 1, 1, 1, 1, 1, 1, 43, 66, 66, 66, 66, 139, 139, 139, 9, 9, 1, 1, 1, 1, 66, 66, 66, 66, 66, 66, 66, 66, 66, 139] 153 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 440 number of broken/clashed sets: 19 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517631 none O=C([O-])C1=CN=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 10, 10, 28, 74, 139, 139, 139, 139, 139, 139, 28, 44, 44, 44, 44, 1, 1, 1, 74, 74, 139, 139, 139, 139, 44, 44, 44, 44, 44, 44, 44, 44, 44, 1] 153 rigid atoms, others: [1, 3, 4, 5, 6, 7, 41, 23, 24, 25] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 432 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517631 none O=C([O-])C1=CN=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [44, 44, 44, 44, 44, 44, 19, 9, 19, 1, 9, 25, 66, 66, 66, 66, 66, 66, 1, 1, 1, 1, 1, 44, 44, 44, 25, 25, 66, 66, 66, 66, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44] 153 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 9, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41]) total number of confs: 205 number of broken/clashed sets: 19 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517631 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517631 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517631/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517631 Building REAL300004517632 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517632' /scratch/stefan/7774842/working/building/REAL300004517632 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517632 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517632/0 /scratch/stefan/7774842/working/building/REAL300004517632 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 672) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/672 `/scratch/stefan/7774842/working/3D/672' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])[C@H]1CC[C@H](C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)CC1) `REAL300004517632.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517632.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517632/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517632 none O=C([O-])[C@H]1CC[C@H](C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [188, 177, 188, 177, 177, 177, 177, 120, 177, 43, 120, 9, 1, 1, 1, 1, 1, 1, 1, 1, 43, 80, 80, 80, 80, 177, 177, 177, 177, 177, 177, 9, 9, 1, 1, 1, 1, 80, 80, 80, 80, 80, 80, 80, 80, 80, 177, 177, 177, 177] 201 rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 736 number of broken/clashed sets: 91 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517632 none O=C([O-])[C@H]1CC[C@H](C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 6, 6, 22, 64, 177, 177, 177, 177, 177, 177, 22, 45, 45, 45, 45, 1, 1, 1, 1, 1, 1, 64, 64, 177, 177, 177, 177, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1, 1, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 46, 47, 48, 49, 25, 26, 27, 28, 29, 30] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 475 number of broken/clashed sets: 91 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517632 none O=C([O-])[C@H]1CC[C@H](C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [72, 45, 72, 45, 45, 45, 45, 24, 45, 9, 24, 1, 9, 26, 80, 80, 80, 80, 80, 80, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45, 45, 26, 26, 80, 80, 80, 80, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45] 201 rigid atoms, others: [43, 37, 38, 39, 40, 41, 42, 11, 44, 45, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 378 number of broken/clashed sets: 91 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517632 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517632 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517632/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517632 Building REAL300004517633 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517633' /scratch/stefan/7774842/working/building/REAL300004517633 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517633 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517633/0 /scratch/stefan/7774842/working/building/REAL300004517633 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 673) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/673 `/scratch/stefan/7774842/working/3D/673' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1CCC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)CC1) `REAL300004517633.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517633.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517633/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517633 none O=C([O-])C1CCC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [165, 156, 165, 156, 156, 156, 104, 40, 104, 9, 1, 1, 1, 1, 1, 1, 1, 1, 40, 82, 82, 82, 82, 156, 156, 156, 156, 156, 156, 156, 156, 9, 9, 1, 1, 1, 1, 82, 82, 82, 82, 82, 82, 82, 82, 82, 156, 156, 156, 156] 201 rigid atoms, others: [33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 650 number of broken/clashed sets: 108 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517633 none O=C([O-])C1CCC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 6, 6, 22, 60, 156, 156, 156, 156, 156, 156, 22, 52, 52, 52, 52, 1, 1, 1, 1, 1, 1, 1, 1, 60, 60, 156, 156, 156, 156, 52, 52, 52, 52, 52, 52, 52, 52, 52, 1, 1, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 46, 47, 48, 49, 23, 24, 25, 26, 27, 28, 29, 30] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 460 number of broken/clashed sets: 108 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517633 none O=C([O-])C1CCC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [81, 50, 81, 52, 52, 52, 27, 8, 27, 1, 8, 26, 82, 82, 82, 82, 82, 82, 1, 1, 1, 1, 1, 52, 52, 52, 52, 52, 52, 52, 52, 26, 26, 82, 82, 82, 82, 1, 1, 1, 1, 1, 1, 1, 1, 1, 52, 52, 52, 52] 201 rigid atoms, others: [37, 38, 39, 40, 9, 42, 43, 44, 45, 18, 19, 20, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 427 number of broken/clashed sets: 108 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517633 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517633 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517633/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517633 Building REAL300004517634 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517634' /scratch/stefan/7774842/working/building/REAL300004517634 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517634 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517634/0 /scratch/stefan/7774842/working/building/REAL300004517634 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 674) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/674 `/scratch/stefan/7774842/working/3D/674' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C1) `REAL300004517634.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517634.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517634/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517634 none O=C([O-])C1=CC=C(CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [145, 145, 145, 145, 145, 145, 138, 64, 34, 64, 8, 1, 1, 1, 1, 1, 1, 1, 1, 34, 40, 40, 40, 40, 145, 145, 145, 145, 138, 138, 8, 8, 1, 1, 1, 1, 40, 40, 40, 40, 40, 40, 40, 40, 40, 145, 145] 146 rigid atoms, others: [32, 33, 34, 35, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 539 number of broken/clashed sets: 58 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517634 none O=C([O-])C1=CC=C(CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 6, 22, 22, 56, 100, 145, 145, 145, 145, 145, 145, 56, 66, 66, 66, 66, 1, 1, 1, 1, 6, 6, 100, 100, 145, 145, 145, 145, 66, 66, 66, 66, 66, 66, 66, 66, 66, 1, 1] 146 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 45, 46, 24, 25, 26, 27] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 499 number of broken/clashed sets: 58 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517634 none O=C([O-])C1=CC=C(CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 47, 14, 6, 14, 1, 6, 16, 40, 40, 40, 40, 40, 40, 1, 1, 1, 1, 1, 50, 50, 50, 50, 47, 47, 16, 16, 40, 40, 40, 40, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 146 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 43, 44, 19, 20, 21, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 243 number of broken/clashed sets: 58 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517634 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517634 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517634/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517634 Building REAL300004517635 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517635' /scratch/stefan/7774842/working/building/REAL300004517635 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517635 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517635/0 /scratch/stefan/7774842/working/building/REAL300004517635 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 675) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/675 `/scratch/stefan/7774842/working/3D/675' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN(CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)N=N1) `REAL300004517635.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517635/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517635 none O=C([O-])C1=CN(CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)N=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [162, 162, 162, 162, 162, 94, 53, 27, 53, 9, 1, 1, 1, 1, 1, 1, 1, 1, 27, 53, 53, 53, 53, 162, 162, 162, 94, 94, 9, 9, 1, 1, 1, 1, 53, 53, 53, 53, 53, 53, 53, 53, 53] 201 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 557 number of broken/clashed sets: 35 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517635 none O=C([O-])C1=CN(CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)N=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 9, 30, 30, 64, 89, 162, 162, 162, 162, 162, 162, 64, 96, 96, 96, 96, 1, 1, 1, 9, 9, 89, 89, 162, 162, 162, 162, 96, 96, 96, 96, 96, 96, 96, 96, 96] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 559 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517635 none O=C([O-])C1=CN(CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)N=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [96, 96, 96, 96, 96, 50, 20, 9, 20, 1, 9, 19, 53, 53, 53, 53, 53, 53, 1, 1, 1, 1, 1, 96, 96, 96, 50, 50, 19, 19, 53, 53, 53, 53, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 9, 42, 18, 19, 20, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 339 number of broken/clashed sets: 35 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517635 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517635 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517635/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517635 Building REAL300004517636 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517636' /scratch/stefan/7774842/working/building/REAL300004517636 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517636 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517636/0 /scratch/stefan/7774842/working/building/REAL300004517636 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 676) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/676 `/scratch/stefan/7774842/working/3D/676' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=CC=C1C(=O)[O-]) `REAL300004517636.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517636/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517636 none CC1=NC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 197 conformations in input total number of sets (complete confs): 197 using faster count positions algorithm for large data unique positions, atoms: [176, 176, 176, 100, 45, 100, 9, 1, 1, 1, 1, 1, 1, 1, 1, 45, 72, 72, 72, 72, 176, 176, 176, 176, 182, 182, 176, 176, 176, 9, 9, 1, 1, 1, 1, 72, 72, 72, 72, 72, 72, 72, 72, 72, 176, 176] 197 rigid atoms, others: [32, 33, 34, 7, 8, 9, 10, 11, 12, 13, 14, 31] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 542 number of broken/clashed sets: 26 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517636 none CC1=NC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 197 conformations in input total number of sets (complete confs): 197 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 10, 10, 30, 80, 176, 176, 176, 176, 176, 176, 30, 48, 48, 48, 48, 1, 1, 1, 1, 3, 3, 2, 2, 2, 80, 80, 176, 176, 176, 176, 48, 48, 48, 48, 48, 48, 48, 48, 48, 1, 1] 197 rigid atoms, others: [0, 1, 2, 3, 4, 44, 45, 20, 21, 22, 23] set([5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 497 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517636 none CC1=NC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 197 conformations in input total number of sets (complete confs): 197 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 48, 21, 10, 21, 1, 10, 27, 72, 72, 72, 72, 72, 72, 1, 1, 1, 1, 1, 48, 48, 48, 48, 68, 68, 48, 48, 48, 27, 27, 72, 72, 72, 72, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48] 197 rigid atoms, others: [35, 36, 37, 6, 39, 40, 41, 42, 43, 15, 16, 17, 18, 19, 38] set([0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45]) total number of confs: 299 number of broken/clashed sets: 26 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517636 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517636 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517636/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517636 Building REAL300004517637 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517637' /scratch/stefan/7774842/working/building/REAL300004517637 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517637 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517637/0 /scratch/stefan/7774842/working/building/REAL300004517637 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 677) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/677 `/scratch/stefan/7774842/working/3D/677' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C1) `REAL300004517637.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517637.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517637/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517637 none O=C([O-])C1=CC=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [98, 94, 98, 94, 98, 98, 94, 41, 94, 9, 1, 1, 1, 1, 1, 1, 1, 1, 41, 57, 57, 57, 57, 98, 98, 98, 98, 9, 9, 1, 1, 1, 1, 57, 57, 57, 57, 57, 57, 57, 57, 57, 98, 98] 106 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 368 number of broken/clashed sets: 17 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517637 none O=C([O-])C1=CC=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 7, 7, 16, 44, 93, 93, 93, 93, 93, 93, 16, 30, 30, 30, 30, 1, 1, 1, 1, 44, 44, 93, 93, 93, 93, 30, 30, 30, 30, 30, 30, 30, 30, 30, 1, 1] 101 rigid atoms, others: [1, 3, 4, 5, 6, 7, 42, 43, 23, 24, 25, 26] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 274 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517637 none O=C([O-])C1=CC=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 106 conformations in input total number of sets (complete confs): 106 using faster count positions algorithm for large data unique positions, atoms: [28, 21, 28, 21, 28, 28, 21, 8, 21, 1, 8, 24, 57, 57, 57, 57, 57, 57, 1, 1, 1, 1, 1, 28, 28, 28, 28, 24, 24, 57, 57, 57, 57, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28] 106 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 9, 18, 19, 20, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43]) total number of confs: 217 number of broken/clashed sets: 17 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517637 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517637 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517637/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517637 Building REAL300004517638 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517638' /scratch/stefan/7774842/working/building/REAL300004517638 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517638 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517638/0 /scratch/stefan/7774842/working/building/REAL300004517638 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 678) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/678 `/scratch/stefan/7774842/working/3D/678' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])[C@@H]1CC[C@H](C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C1) `REAL300004517638.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517638/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517638 none O=C([O-])[C@@H]1CC[C@H](C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [185, 169, 185, 169, 169, 169, 169, 90, 169, 41, 90, 9, 1, 1, 1, 1, 1, 1, 1, 1, 41, 64, 64, 64, 64, 169, 169, 169, 169, 169, 9, 9, 1, 1, 1, 1, 64, 64, 64, 64, 64, 64, 64, 64, 64, 169, 169] 201 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 658 number of broken/clashed sets: 87 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517638 none O=C([O-])[C@@H]1CC[C@H](C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 25, 70, 169, 169, 169, 169, 169, 169, 25, 43, 43, 43, 43, 1, 1, 1, 1, 1, 70, 70, 169, 169, 169, 169, 43, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 45, 46, 25, 26, 27, 28, 29] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 474 number of broken/clashed sets: 87 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517638 none O=C([O-])[C@@H]1CC[C@H](C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 43, 59, 43, 43, 43, 43, 21, 43, 8, 21, 1, 8, 22, 64, 64, 64, 64, 64, 64, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 22, 22, 64, 64, 64, 64, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43] 201 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 288 number of broken/clashed sets: 87 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517638 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517638 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517638/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517638 Building REAL300004517639 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517639' /scratch/stefan/7774842/working/building/REAL300004517639 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517639 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517639/0 /scratch/stefan/7774842/working/building/REAL300004517639 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 679) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/679 `/scratch/stefan/7774842/working/3D/679' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=CC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=C1) `REAL300004517639.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517639.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517639/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517639 none O=C([O-])CC1=CC=CC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [192, 191, 192, 159, 159, 115, 159, 159, 77, 38, 77, 9, 1, 1, 1, 1, 1, 1, 1, 1, 38, 51, 51, 51, 51, 159, 191, 191, 150, 159, 159, 9, 9, 1, 1, 1, 1, 51, 51, 51, 51, 51, 51, 51, 51, 51, 159] 201 rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 782 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517639 none O=C([O-])CC1=CC=CC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [7, 2, 7, 1, 1, 1, 1, 1, 1, 1, 10, 10, 29, 70, 159, 159, 159, 159, 159, 159, 29, 40, 40, 40, 40, 1, 2, 2, 1, 1, 1, 70, 70, 159, 159, 159, 159, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1] 201 rigid atoms, others: [3, 4, 5, 6, 7, 8, 9, 46, 25, 28, 29, 30] set([0, 1, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 444 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517639 none O=C([O-])CC1=CC=CC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [82, 53, 82, 40, 40, 25, 40, 40, 16, 7, 16, 1, 7, 21, 51, 51, 51, 51, 51, 51, 1, 1, 1, 1, 1, 40, 53, 53, 36, 40, 40, 21, 21, 51, 51, 51, 51, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40] 201 rigid atoms, others: [43, 37, 38, 39, 40, 41, 42, 11, 44, 45, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46]) total number of confs: 407 number of broken/clashed sets: 16 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517639 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517639 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517639/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517639 Building REAL300004517640 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517640' /scratch/stefan/7774842/working/building/REAL300004517640 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517640 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517640/0 /scratch/stefan/7774842/working/building/REAL300004517640 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 680) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/680 `/scratch/stefan/7774842/working/3D/680' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=CO1) `REAL300004517640.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517640.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517640/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517640 none O=C([O-])CC1=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=CO1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [137, 129, 137, 124, 124, 84, 41, 84, 9, 1, 1, 1, 1, 1, 1, 1, 1, 41, 77, 77, 77, 77, 124, 124, 124, 129, 129, 9, 9, 1, 1, 1, 1, 77, 77, 77, 77, 77, 77, 77, 77, 77, 124, 124] 164 rigid atoms, others: [32, 9, 10, 11, 12, 13, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 501 number of broken/clashed sets: 45 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517640 none O=C([O-])CC1=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=CO1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [7, 2, 7, 1, 1, 1, 1, 8, 8, 19, 52, 124, 124, 124, 124, 124, 124, 19, 38, 38, 38, 38, 1, 1, 1, 2, 2, 52, 52, 124, 124, 124, 124, 38, 38, 38, 38, 38, 38, 38, 38, 38, 1, 1] 164 rigid atoms, others: [3, 4, 5, 6, 42, 43, 22, 23, 24] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 382 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517640 none O=C([O-])CC1=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=CO1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 164 conformations in input total number of sets (complete confs): 164 using faster count positions algorithm for large data unique positions, atoms: [51, 39, 51, 38, 38, 21, 8, 21, 1, 8, 25, 77, 77, 77, 77, 77, 77, 1, 1, 1, 1, 1, 38, 38, 38, 39, 39, 25, 25, 77, 77, 77, 77, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38] 164 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 8, 41, 17, 18, 19, 20, 21, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43]) total number of confs: 281 number of broken/clashed sets: 45 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517640 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517640 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517640/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517640 Building REAL300004517641 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517641' /scratch/stefan/7774842/working/building/REAL300004517641 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517641 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517641/0 /scratch/stefan/7774842/working/building/REAL300004517641 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 681) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/681 `/scratch/stefan/7774842/working/3D/681' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=COC(CC(=O)[O-])=C1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1) `REAL300004517641.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517641.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517641/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517641 none CC1=COC(CC(=O)[O-])=C1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 5, 1, 11, 11, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 63, 63, 63, 67, 67, 67, 48, 35, 48, 9, 1, 1, 1, 1, 1, 1, 1, 1, 35, 40, 40, 40, 40, 63, 63, 63, 63, 67, 67, 9, 9, 1, 1, 1, 1, 40, 40, 40, 40, 40, 40, 40, 40, 40] 67 rigid atoms, others: [34, 35, 36, 37, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 209 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517641 none CC1=COC(CC(=O)[O-])=C1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 5, 1, 11, 11, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 3, 7, 7, 1, 1, 7, 7, 15, 28, 63, 63, 63, 63, 63, 63, 15, 18, 18, 18, 18, 2, 2, 2, 1, 3, 3, 28, 28, 63, 63, 63, 63, 18, 18, 18, 18, 18, 18, 18, 18, 18] 67 rigid atoms, others: [0, 1, 2, 3, 4, 5, 9, 10, 29] set([6, 7, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 201 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517641 none CC1=COC(CC(=O)[O-])=C1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 5, 1, 11, 11, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [18, 18, 18, 18, 18, 18, 19, 25, 25, 11, 6, 11, 1, 6, 16, 40, 40, 40, 40, 40, 40, 1, 1, 1, 1, 1, 18, 18, 18, 18, 19, 19, 16, 16, 40, 40, 40, 40, 1, 1, 1, 1, 1, 1, 1, 1, 1] 67 rigid atoms, others: [38, 39, 40, 41, 42, 43, 12, 45, 46, 44, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 146 number of broken/clashed sets: 14 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517641 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517641 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517641/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517641 Building REAL300004517642 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517642' /scratch/stefan/7774842/working/building/REAL300004517642 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517642 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517642/0 /scratch/stefan/7774842/working/building/REAL300004517642 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 682) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/682 `/scratch/stefan/7774842/working/3D/682' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=NC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=C1) `REAL300004517642.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517642.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517642/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517642 none O=C([O-])C1=CC=NC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [186, 186, 186, 186, 186, 186, 186, 88, 43, 88, 9, 1, 1, 1, 1, 1, 1, 1, 1, 43, 66, 66, 66, 66, 186, 186, 186, 9, 9, 1, 1, 1, 1, 66, 66, 66, 66, 66, 66, 66, 66, 66, 186] 201 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 503 number of broken/clashed sets: 17 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517642 none O=C([O-])C1=CC=NC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 34, 98, 186, 186, 186, 186, 186, 186, 34, 56, 56, 56, 56, 1, 1, 1, 98, 98, 186, 186, 186, 186, 56, 56, 56, 56, 56, 56, 56, 56, 56, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 42, 24, 25, 26] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 581 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517642 none O=C([O-])C1=CC=NC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 56, 56, 56, 56, 56, 18, 8, 18, 1, 8, 24, 66, 66, 66, 66, 66, 66, 1, 1, 1, 1, 1, 56, 56, 56, 24, 24, 66, 66, 66, 66, 1, 1, 1, 1, 1, 1, 1, 1, 1, 56] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 10, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42]) total number of confs: 219 number of broken/clashed sets: 17 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517642 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517642 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517642/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517642 Building REAL300004517643 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517643' /scratch/stefan/7774842/working/building/REAL300004517643 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517643 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517643/0 /scratch/stefan/7774842/working/building/REAL300004517643 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 683) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/683 `/scratch/stefan/7774842/working/3D/683' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1CCC(CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)CC1) `REAL300004517643.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517643/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517643 none O=C([O-])C1CCC(CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [196, 170, 196, 170, 170, 170, 112, 58, 33, 58, 9, 1, 1, 1, 1, 1, 1, 1, 1, 33, 51, 51, 51, 51, 170, 170, 170, 170, 170, 170, 170, 170, 112, 112, 9, 9, 1, 1, 1, 1, 51, 51, 51, 51, 51, 51, 51, 51, 51, 170, 170, 170, 170] 201 rigid atoms, others: [36, 37, 38, 39, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 815 number of broken/clashed sets: 178 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517643 none O=C([O-])C1CCC(CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 5, 15, 15, 46, 89, 170, 170, 170, 170, 170, 170, 46, 80, 80, 80, 80, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 89, 89, 170, 170, 170, 170, 80, 80, 80, 80, 80, 80, 80, 80, 80, 1, 1, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 49, 50, 51, 52, 24, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 566 number of broken/clashed sets: 178 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517643 none O=C([O-])C1CCC(CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [100, 80, 100, 80, 80, 80, 47, 19, 7, 19, 1, 7, 25, 51, 51, 51, 51, 51, 51, 1, 1, 1, 1, 1, 80, 80, 80, 80, 80, 80, 80, 80, 47, 47, 25, 25, 51, 51, 51, 51, 1, 1, 1, 1, 1, 1, 1, 1, 1, 80, 80, 80, 80] 201 rigid atoms, others: [40, 41, 10, 43, 44, 45, 46, 47, 48, 19, 20, 21, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 485 number of broken/clashed sets: 178 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517643 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517643 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517643/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517643 Building REAL300004517644 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517644' /scratch/stefan/7774842/working/building/REAL300004517644 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517644 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517644/0 /scratch/stefan/7774842/working/building/REAL300004517644 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 684) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/684 `/scratch/stefan/7774842/working/3D/684' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(CC(=O)[O-])CC(=O)N(CC1=CC=CC(F)=C1)C1CCCC1) `REAL300004517644.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517644.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517644/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517644 none CC(C)(CC(=O)[O-])CC(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [22, 15, 22, 22, 25, 28, 28, 12, 5, 12, 1, 5, 15, 39, 39, 39, 39, 39, 39, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 22, 25, 25, 15, 15, 15, 15, 39, 39, 39, 39, 1, 1, 1, 1, 1, 1, 1, 1, 1] 82 rigid atoms, others: [40, 41, 10, 43, 44, 45, 46, 47, 48, 19, 20, 21, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 191 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517644 none CC(C)(CC(=O)[O-])CC(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 82 conformations in input total number of sets (complete confs): 82 using faster count positions algorithm for large data unique positions, atoms: [80, 66, 80, 80, 80, 80, 80, 54, 35, 54, 8, 1, 1, 1, 1, 1, 1, 1, 1, 35, 39, 39, 39, 39, 80, 80, 80, 80, 80, 80, 80, 80, 66, 66, 8, 8, 1, 1, 1, 1, 39, 39, 39, 39, 39, 39, 39, 39, 39] 82 rigid atoms, others: [36, 37, 38, 39, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 333 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517644 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517644 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517644/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517644 Building REAL300004517645 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517645' /scratch/stefan/7774842/working/building/REAL300004517645 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517645 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517645/0 /scratch/stefan/7774842/working/building/REAL300004517645 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 685) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/685 `/scratch/stefan/7774842/working/3D/685' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CCCC(=O)N(CC1=CC=CC(F)=C1)C1CCCC1) `REAL300004517645.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517645/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517645 none O=C([O-])CCCC(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [11, 7, 11, 7, 5, 5, 3, 5, 1, 3, 7, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 7, 7, 7, 7, 5, 5, 7, 7, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1] 28 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 41, 42, 17, 18, 19, 20, 21, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 75 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517645 none O=C([O-])CCCC(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 21, 21, 16, 21, 6, 1, 1, 1, 1, 1, 1, 1, 1, 16, 17, 17, 17, 17, 28, 28, 28, 28, 21, 21, 6, 6, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 17] 28 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 117 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517645 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517645 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517645/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517645 Building REAL300004517646 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517646' /scratch/stefan/7774842/working/building/REAL300004517646 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517646 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517646/0 /scratch/stefan/7774842/working/building/REAL300004517646 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 686) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/686 `/scratch/stefan/7774842/working/3D/686' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(CC(=O)[O-])CC(=O)N(CC1=CC=CC(F)=C1)C1CCCC1) `REAL300004517646.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517646.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517646/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517646 none CC(CC(=O)[O-])CC(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 11, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [9, 8, 9, 10, 14, 14, 7, 4, 7, 1, 4, 10, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 9, 9, 9, 9, 10, 10, 8, 8, 10, 10, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1] 38 rigid atoms, others: [37, 38, 39, 40, 9, 42, 43, 44, 45, 18, 19, 20, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 98 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517646 none CC(CC(=O)[O-])CC(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 11, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [38, 31, 38, 38, 38, 38, 26, 21, 26, 7, 1, 1, 1, 1, 1, 1, 1, 1, 21, 23, 23, 23, 23, 38, 38, 38, 38, 38, 38, 31, 31, 7, 7, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23] 38 rigid atoms, others: [33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 162 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517646 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517646 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517646/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517646 Building REAL300004517647 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517647' /scratch/stefan/7774842/working/building/REAL300004517647 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517647 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517647/0 /scratch/stefan/7774842/working/building/REAL300004517647 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 687) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/687 `/scratch/stefan/7774842/working/3D/687' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C2N=CC=C(C(=O)N(CC3=CC=CC(F)=C3)C3CCCC3)N2N=C1) `REAL300004517647.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517647.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517647/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517647 none O=C([O-])C1=C2N=CC=C(C(=O)N(CC3=CC=CC(F)=C3)C3CCCC3)N2N=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 190 conformations in input total number of sets (complete confs): 190 using faster count positions algorithm for large data unique positions, atoms: [154, 152, 154, 152, 152, 152, 152, 152, 79, 36, 79, 9, 1, 1, 1, 1, 1, 1, 1, 1, 36, 66, 66, 66, 66, 152, 152, 152, 152, 152, 9, 9, 1, 1, 1, 1, 66, 66, 66, 66, 66, 66, 66, 66, 66, 152] 190 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 458 number of broken/clashed sets: 31 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517647 none O=C([O-])C1=C2N=CC=C(C(=O)N(CC3=CC=CC(F)=C3)C3CCCC3)N2N=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 190 conformations in input total number of sets (complete confs): 190 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 9, 9, 26, 66, 152, 152, 152, 152, 152, 152, 26, 52, 52, 52, 52, 1, 1, 1, 1, 1, 66, 66, 152, 152, 152, 152, 52, 52, 52, 52, 52, 52, 52, 52, 52, 1] 190 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 45, 25, 26, 27, 28, 29] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 457 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517647 none O=C([O-])C1=C2N=CC=C(C(=O)N(CC3=CC=CC(F)=C3)C3CCCC3)N2N=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 8, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 190 conformations in input total number of sets (complete confs): 190 using faster count positions algorithm for large data unique positions, atoms: [64, 52, 64, 52, 52, 52, 52, 52, 22, 9, 22, 1, 9, 24, 66, 66, 66, 66, 66, 66, 1, 1, 1, 1, 1, 52, 52, 52, 52, 52, 24, 24, 66, 66, 66, 66, 1, 1, 1, 1, 1, 1, 1, 1, 1, 52] 190 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45]) total number of confs: 270 number of broken/clashed sets: 31 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517647 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517647 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517647/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517647 Building REAL300004517648 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517648' /scratch/stefan/7774842/working/building/REAL300004517648 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517648 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517648/0 /scratch/stefan/7774842/working/building/REAL300004517648 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 688) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/688 `/scratch/stefan/7774842/working/3D/688' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)NC2=CC=CC=C21) `REAL300004517648.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517648.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517648/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517648 none O=C([O-])CC1=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)NC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [84, 82, 84, 82, 82, 61, 37, 61, 9, 1, 1, 1, 1, 1, 1, 1, 1, 37, 49, 49, 49, 49, 82, 82, 82, 82, 82, 82, 82, 82, 82, 9, 9, 1, 1, 1, 1, 49, 49, 49, 49, 49, 49, 49, 49, 49, 82, 82, 82, 82, 82] 90 rigid atoms, others: [33, 34, 35, 36, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 280 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517648 none O=C([O-])CC1=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)NC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [7, 2, 7, 1, 1, 1, 1, 7, 7, 17, 38, 82, 82, 82, 82, 82, 82, 17, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 1, 2, 2, 38, 38, 82, 82, 82, 82, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1] 90 rigid atoms, others: [3, 4, 5, 6, 46, 47, 48, 49, 50, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 264 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517648 none O=C([O-])CC1=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)NC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [30, 25, 30, 25, 25, 13, 7, 13, 1, 7, 19, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 19, 19, 49, 49, 49, 49, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25] 90 rigid atoms, others: [37, 38, 39, 8, 41, 42, 43, 44, 45, 17, 18, 19, 20, 21, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 160 number of broken/clashed sets: 9 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517648 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517648 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517648/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517648 Building REAL300004517649 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517649' /scratch/stefan/7774842/working/building/REAL300004517649 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517649 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517649/0 /scratch/stefan/7774842/working/building/REAL300004517649 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 689) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/689 `/scratch/stefan/7774842/working/3D/689' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=NO1) `REAL300004517649.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517649.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517649/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517649 none O=C([O-])C1=CC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=NO1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [164, 164, 164, 164, 164, 82, 34, 82, 9, 1, 1, 1, 1, 1, 1, 1, 1, 34, 69, 69, 69, 69, 164, 164, 164, 9, 9, 1, 1, 1, 1, 69, 69, 69, 69, 69, 69, 69, 69, 69] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 478 number of broken/clashed sets: 41 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517649 none O=C([O-])C1=CC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=NO1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 12, 12, 43, 89, 164, 164, 164, 164, 164, 164, 43, 77, 77, 77, 77, 1, 1, 1, 89, 89, 164, 164, 164, 164, 77, 77, 77, 77, 77, 77, 77, 77, 77] 201 rigid atoms, others: [1, 3, 4, 5, 6, 22, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 556 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517649 none O=C([O-])C1=CC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=NO1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 77, 77, 77, 25, 10, 25, 1, 10, 29, 69, 69, 69, 69, 69, 69, 1, 1, 1, 1, 1, 77, 77, 77, 29, 29, 69, 69, 69, 69, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 8, 17, 18, 19, 20, 21, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 272 number of broken/clashed sets: 41 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517649 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517649 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517649/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517649 Building REAL300004517650 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517650' /scratch/stefan/7774842/working/building/REAL300004517650 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517650 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517650/0 /scratch/stefan/7774842/working/building/REAL300004517650 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 690) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/690 `/scratch/stefan/7774842/working/3D/690' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C(C(=O)[O-])O1) `REAL300004517650.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517650/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517650 none CC1=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [168, 168, 104, 41, 104, 9, 1, 1, 1, 1, 1, 1, 1, 1, 41, 75, 75, 75, 75, 168, 168, 168, 168, 168, 168, 168, 168, 168, 9, 9, 1, 1, 1, 1, 75, 75, 75, 75, 75, 75, 75, 75, 75, 168] 183 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 537 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517650 none CC1=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 9, 9, 29, 82, 168, 168, 168, 168, 168, 168, 29, 52, 52, 52, 52, 1, 1, 1, 1, 1, 1, 2, 2, 2, 82, 82, 168, 168, 168, 168, 52, 52, 52, 52, 52, 52, 52, 52, 52, 1] 183 rigid atoms, others: [0, 1, 2, 3, 43, 19, 20, 21, 22, 23, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 516 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517650 none CC1=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 183 conformations in input total number of sets (complete confs): 183 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 21, 9, 21, 1, 9, 28, 75, 75, 75, 75, 75, 75, 1, 1, 1, 1, 1, 52, 52, 52, 52, 52, 52, 52, 52, 52, 28, 28, 75, 75, 75, 75, 1, 1, 1, 1, 1, 1, 1, 1, 1, 52] 183 rigid atoms, others: [34, 35, 36, 5, 38, 39, 40, 41, 42, 14, 15, 16, 17, 18, 37] set([0, 1, 2, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43]) total number of confs: 242 number of broken/clashed sets: 33 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517650 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517650 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517650/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517650 Building REAL300004517651 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517651' /scratch/stefan/7774842/working/building/REAL300004517651 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517651 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517651/0 /scratch/stefan/7774842/working/building/REAL300004517651 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 691) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/691 `/scratch/stefan/7774842/working/3D/691' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])OC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=C1) `REAL300004517651.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517651.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517651/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517651 none CC1=C(C(=O)[O-])OC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [177, 177, 177, 177, 186, 186, 177, 100, 44, 100, 9, 1, 1, 1, 1, 1, 1, 1, 1, 44, 76, 76, 76, 76, 177, 177, 177, 177, 9, 9, 1, 1, 1, 1, 76, 76, 76, 76, 76, 76, 76, 76, 76, 177] 201 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 564 number of broken/clashed sets: 21 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517651 none CC1=C(C(=O)[O-])OC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 9, 9, 27, 71, 177, 177, 177, 177, 177, 177, 27, 43, 43, 43, 43, 1, 2, 2, 2, 71, 71, 177, 177, 177, 177, 43, 43, 43, 43, 43, 43, 43, 43, 43, 1] 201 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 43, 24] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 467 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517651 none CC1=C(C(=O)[O-])OC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 43, 61, 61, 43, 21, 10, 21, 1, 10, 27, 76, 76, 76, 76, 76, 76, 1, 1, 1, 1, 1, 43, 43, 43, 43, 27, 27, 76, 76, 76, 76, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 10, 19, 20, 21, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43]) total number of confs: 294 number of broken/clashed sets: 21 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517651 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517651 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517651/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517651 Building REAL300004517652 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517652' /scratch/stefan/7774842/working/building/REAL300004517652 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517652 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517652/0 /scratch/stefan/7774842/working/building/REAL300004517652 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 692) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/692 `/scratch/stefan/7774842/working/3D/692' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN(CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)N=C1) `REAL300004517652.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517652 none O=C([O-])C1=CN(CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)N=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [164, 164, 164, 164, 164, 93, 51, 28, 51, 9, 1, 1, 1, 1, 1, 1, 1, 1, 28, 54, 54, 54, 54, 164, 164, 164, 93, 93, 9, 9, 1, 1, 1, 1, 54, 54, 54, 54, 54, 54, 54, 54, 54, 164] 201 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 561 number of broken/clashed sets: 38 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517652 none O=C([O-])C1=CN(CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)N=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 9, 26, 26, 59, 87, 164, 164, 164, 164, 164, 164, 59, 91, 91, 91, 91, 1, 1, 1, 9, 9, 87, 87, 164, 164, 164, 164, 91, 91, 91, 91, 91, 91, 91, 91, 91, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 43, 23, 24, 25] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 551 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517652 none O=C([O-])C1=CN(CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)N=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [91, 91, 91, 91, 91, 48, 21, 10, 21, 1, 10, 22, 54, 54, 54, 54, 54, 54, 1, 1, 1, 1, 1, 91, 91, 91, 48, 48, 22, 22, 54, 54, 54, 54, 1, 1, 1, 1, 1, 1, 1, 1, 1, 91] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 9, 42, 18, 19, 20, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43]) total number of confs: 339 number of broken/clashed sets: 38 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517652 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517652 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517652/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517652 Building REAL300004517653 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517653' /scratch/stefan/7774842/working/building/REAL300004517653 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517653 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517653/0 /scratch/stefan/7774842/working/building/REAL300004517653 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 693) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/693 `/scratch/stefan/7774842/working/3D/693' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=CC1=CC=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)O1) `REAL300004517653.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517653.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517653/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517653 none O=C([O-])C=CC1=CC=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [166, 162, 166, 162, 106, 106, 106, 106, 62, 29, 62, 9, 1, 1, 1, 1, 1, 1, 1, 1, 29, 56, 56, 56, 56, 106, 162, 162, 106, 106, 9, 9, 1, 1, 1, 1, 56, 56, 56, 56, 56, 56, 56, 56, 56] 201 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 551 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517653 none O=C([O-])C=CC1=CC=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 9, 14, 9, 1, 1, 1, 1, 1, 1, 6, 6, 22, 48, 106, 106, 106, 106, 106, 106, 22, 42, 42, 42, 42, 1, 9, 9, 1, 1, 48, 48, 106, 106, 106, 106, 42, 42, 42, 42, 42, 42, 42, 42, 42] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 25, 28, 29] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 367 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517653 none O=C([O-])C=CC1=CC=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [93, 77, 93, 77, 42, 42, 42, 42, 21, 10, 21, 1, 10, 20, 56, 56, 56, 56, 56, 56, 1, 1, 1, 1, 1, 42, 77, 77, 42, 42, 20, 20, 56, 56, 56, 56, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 347 number of broken/clashed sets: 11 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517653 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517653 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517653/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517653 Building REAL300004517654 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517654' /scratch/stefan/7774842/working/building/REAL300004517654 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517654 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517654/0 /scratch/stefan/7774842/working/building/REAL300004517654 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 694) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/694 `/scratch/stefan/7774842/working/3D/694' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COC1=CC=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C1) `REAL300004517654.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517654.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517654/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517654 none O=C([O-])COC1=CC=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [188, 188, 188, 133, 60, 34, 70, 70, 34, 24, 34, 7, 1, 1, 1, 1, 1, 1, 1, 1, 24, 28, 28, 28, 28, 70, 70, 188, 188, 70, 70, 7, 7, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28, 28, 70, 70] 201 rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 754 number of broken/clashed sets: 19 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517654 none O=C([O-])COC1=CC=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 9, 14, 3, 1, 1, 1, 1, 1, 1, 8, 8, 18, 36, 70, 70, 70, 70, 70, 70, 18, 22, 22, 22, 22, 1, 1, 9, 9, 1, 1, 36, 36, 70, 70, 70, 70, 22, 22, 22, 22, 22, 22, 22, 22, 22, 1, 1] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 46, 47, 25, 26, 29, 30] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 255 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517654 none O=C([O-])COC1=CC=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 85, 90, 44, 16, 10, 22, 22, 10, 4, 10, 1, 4, 12, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 22, 22, 85, 85, 22, 22, 12, 12, 28, 28, 28, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22] 201 rigid atoms, others: [43, 37, 38, 39, 40, 41, 42, 11, 44, 45, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 402 number of broken/clashed sets: 19 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517654 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517654 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517654/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517654 Building REAL300004517655 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517655' /scratch/stefan/7774842/working/building/REAL300004517655 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517655 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517655/0 /scratch/stefan/7774842/working/building/REAL300004517655 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 695) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/695 `/scratch/stefan/7774842/working/3D/695' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CSCCC(=O)N(CC1=CC=CC(F)=C1)C1CCCC1) `REAL300004517655.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517655/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517655 none O=C([O-])CSCCC(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 14, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [67, 61, 67, 40, 24, 17, 10, 4, 10, 1, 4, 14, 41, 41, 41, 41, 41, 41, 1, 1, 1, 1, 1, 61, 61, 24, 24, 17, 17, 14, 14, 41, 41, 41, 41, 1, 1, 1, 1, 1, 1, 1, 1, 1] 188 rigid atoms, others: [35, 36, 37, 38, 39, 40, 9, 42, 43, 18, 19, 20, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 341 number of broken/clashed sets: 22 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517655 none O=C([O-])CSCCC(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'S.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 14, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [180, 179, 180, 170, 107, 84, 58, 36, 58, 8, 1, 1, 1, 1, 1, 1, 1, 1, 36, 41, 41, 41, 41, 179, 179, 107, 107, 84, 84, 8, 8, 1, 1, 1, 1, 41, 41, 41, 41, 41, 41, 41, 41, 41] 188 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 632 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517655 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517655 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517655/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517655 Building REAL300004517656 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517656' /scratch/stefan/7774842/working/building/REAL300004517656 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517656 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517656/0 /scratch/stefan/7774842/working/building/REAL300004517656 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 696) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/696 `/scratch/stefan/7774842/working/3D/696' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)N=C1) `REAL300004517656.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517656 none O=C([O-])C1=CC=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)N=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [146, 146, 146, 146, 146, 146, 92, 43, 92, 9, 1, 1, 1, 1, 1, 1, 1, 1, 43, 66, 66, 66, 66, 146, 146, 146, 146, 9, 9, 1, 1, 1, 1, 66, 66, 66, 66, 66, 66, 66, 66, 66, 146] 159 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 450 number of broken/clashed sets: 19 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517656 none O=C([O-])C1=CC=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)N=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 29, 75, 146, 146, 146, 146, 146, 146, 29, 47, 47, 47, 47, 1, 1, 1, 1, 75, 75, 146, 146, 146, 146, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1] 159 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 42, 23, 24, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 445 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517656 none O=C([O-])C1=CC=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)N=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 159 conformations in input total number of sets (complete confs): 159 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 47, 47, 47, 47, 19, 9, 19, 1, 9, 25, 66, 66, 66, 66, 66, 66, 1, 1, 1, 1, 1, 47, 47, 47, 47, 25, 25, 66, 66, 66, 66, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47] 159 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 9, 18, 19, 20, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42]) total number of confs: 210 number of broken/clashed sets: 19 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517656 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517656 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517656/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517656 Building REAL300004517657 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517657' /scratch/stefan/7774842/working/building/REAL300004517657 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517657 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517657/0 /scratch/stefan/7774842/working/building/REAL300004517657 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 697) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/697 `/scratch/stefan/7774842/working/3D/697' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])COCC(=O)N(CC1=CC=CC(F)=C1)C1CCCC1) `REAL300004517657.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517657/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517657 none O=C([O-])COCC(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [16, 13, 16, 12, 9, 6, 3, 6, 1, 3, 9, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 13, 13, 9, 9, 9, 9, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1] 35 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 8, 17, 18, 19, 20, 21, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 96 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517657 none O=C([O-])COCC(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 12, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 28, 26, 19, 26, 6, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 35, 35, 28, 28, 6, 6, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19] 35 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 111 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517657 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517657 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517657/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517657 Building REAL300004517658 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517658' /scratch/stefan/7774842/working/building/REAL300004517658 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517658 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517658/0 /scratch/stefan/7774842/working/building/REAL300004517658 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 698) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/698 `/scratch/stefan/7774842/working/3D/698' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1N=C(C(=O)[O-])C=C1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1) `REAL300004517658.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517658.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) Traceback (most recent call last): File "/nfs/home/rstein/zzz.github/DOCK/ligand/amsol/process_amsol_mol2.py", line 476, in main() File "/nfs/home/rstein/zzz.github/DOCK/ligand/amsol/process_amsol_mol2.py", line 458, in main diff_amsol71_files(atom_list_wat, tot_wat, atom_list_hex, tot_hex, name_wat, numat_wat, outputprefix) File "/nfs/home/rstein/zzz.github/DOCK/ligand/amsol/process_amsol_mol2.py", line 273, in diff_amsol71_files Sigmahex[i] = float(atom_listhex[i][5]) # Sigma (kcal/Ang**2) ValueError: could not convert string to float: ******* Solvation calculation failed Skipping REAL300004517658 0 /scratch/stefan/7774842/working/building/REAL300004517658 /scratch/stefan/7774842/working /scratch/stefan/7774842 `0' -> `0.failed' Finished preparing REAL300004517658 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Found failed protomers Marking REAL300004517658 as failed mkdir: created directory `/scratch/stefan/7774842/failed' `/scratch/stefan/7774842/working/building/REAL300004517658' -> `/scratch/stefan/7774842/failed/REAL300004517658' Building REAL300004517659 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517659' /scratch/stefan/7774842/working/building/REAL300004517659 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517659 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517659/0 /scratch/stefan/7774842/working/building/REAL300004517659 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 699) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/699 `/scratch/stefan/7774842/working/3D/699' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H](C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)O[C@H]1C(=O)[O-]) `REAL300004517659.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517659.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517659/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517659 none C[C@@H]1C[C@H](C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)O[C@H]1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 12, 5, 7, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 136 conformations in input total number of sets (complete confs): 136 using faster count positions algorithm for large data unique positions, atoms: [116, 116, 116, 116, 79, 116, 41, 79, 9, 1, 1, 1, 1, 1, 1, 1, 1, 41, 60, 60, 60, 60, 116, 116, 116, 116, 128, 128, 116, 116, 116, 116, 116, 9, 9, 1, 1, 1, 1, 60, 60, 60, 60, 60, 60, 60, 60, 60] 136 rigid atoms, others: [35, 36, 37, 38, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 490 number of broken/clashed sets: 22 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517659 none C[C@@H]1C[C@H](C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)O[C@H]1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 12, 5, 7, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 136 conformations in input total number of sets (complete confs): 136 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 6, 6, 15, 46, 116, 116, 116, 116, 116, 116, 15, 28, 28, 28, 28, 1, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 46, 46, 116, 116, 116, 116, 28, 28, 28, 28, 28, 28, 28, 28, 28] 136 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 22, 23, 24, 25, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 26, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 320 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517659 none C[C@@H]1C[C@H](C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)O[C@H]1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 12, 5, 7, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 136 conformations in input total number of sets (complete confs): 136 using faster count positions algorithm for large data unique positions, atoms: [28, 28, 28, 28, 18, 28, 7, 18, 1, 7, 21, 60, 60, 60, 60, 60, 60, 1, 1, 1, 1, 1, 28, 28, 28, 28, 37, 37, 28, 28, 28, 28, 28, 21, 21, 60, 60, 60, 60, 1, 1, 1, 1, 1, 1, 1, 1, 1] 136 rigid atoms, others: [39, 8, 41, 42, 43, 44, 45, 46, 47, 17, 18, 19, 20, 21, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 229 number of broken/clashed sets: 22 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517659 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517659 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517659/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517659 Building REAL300004517660 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517660' /scratch/stefan/7774842/working/building/REAL300004517660 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517660 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517660/0 /scratch/stefan/7774842/working/building/REAL300004517660 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 700) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/700 `/scratch/stefan/7774842/working/3D/700' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=CC=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C1) `REAL300004517660.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517660/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517660 none O=C([O-])CC1=CC=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 197 conformations in input total number of sets (complete confs): 197 using faster count positions algorithm for large data unique positions, atoms: [186, 184, 186, 180, 154, 184, 184, 108, 42, 108, 9, 1, 1, 1, 1, 1, 1, 1, 1, 42, 66, 66, 66, 66, 184, 184, 184, 184, 184, 184, 9, 9, 1, 1, 1, 1, 66, 66, 66, 66, 66, 66, 66, 66, 66, 184, 184] 197 rigid atoms, others: [32, 33, 34, 35, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 724 number of broken/clashed sets: 29 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517660 none O=C([O-])CC1=CC=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 197 conformations in input total number of sets (complete confs): 197 using faster count positions algorithm for large data unique positions, atoms: [4, 2, 4, 1, 1, 1, 1, 1, 1, 8, 8, 22, 74, 184, 184, 184, 184, 184, 184, 22, 43, 43, 43, 43, 1, 1, 2, 2, 1, 1, 74, 74, 184, 184, 184, 184, 43, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1] 197 rigid atoms, others: [3, 4, 5, 6, 7, 8, 45, 46, 24, 25, 28, 29] set([0, 1, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 512 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517660 none O=C([O-])CC1=CC=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 197 conformations in input total number of sets (complete confs): 197 using faster count positions algorithm for large data unique positions, atoms: [68, 43, 68, 34, 24, 43, 43, 21, 8, 21, 1, 8, 25, 66, 66, 66, 66, 66, 66, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 43, 25, 25, 66, 66, 66, 66, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43] 197 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 43, 44, 19, 20, 21, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 398 number of broken/clashed sets: 29 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517660 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517660 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517660/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517660 Building REAL300004517661 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517661' /scratch/stefan/7774842/working/building/REAL300004517661 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517661 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517661/0 /scratch/stefan/7774842/working/building/REAL300004517661 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 701) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/701 `/scratch/stefan/7774842/working/3D/701' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C=CC1=CC=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C1) `REAL300004517661.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517661 none O=C([O-])C=CC1=CC=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [190, 189, 190, 189, 180, 144, 180, 180, 74, 38, 74, 9, 1, 1, 1, 1, 1, 1, 1, 1, 38, 52, 52, 52, 52, 180, 180, 189, 189, 180, 180, 9, 9, 1, 1, 1, 1, 52, 52, 52, 52, 52, 52, 52, 52, 52, 180, 180] 201 rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 672 number of broken/clashed sets: 17 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517661 none O=C([O-])C=CC1=CC=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [8, 3, 8, 3, 1, 1, 1, 1, 1, 1, 10, 10, 29, 77, 180, 180, 180, 180, 180, 180, 29, 46, 46, 46, 46, 1, 1, 3, 3, 1, 1, 77, 77, 180, 180, 180, 180, 46, 46, 46, 46, 46, 46, 46, 46, 46, 1, 1] 201 rigid atoms, others: [4, 5, 6, 7, 8, 9, 46, 47, 25, 26, 29, 30] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 509 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517661 none O=C([O-])C=CC1=CC=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 62, 73, 62, 46, 29, 46, 46, 15, 7, 15, 1, 7, 21, 52, 52, 52, 52, 52, 52, 1, 1, 1, 1, 1, 46, 46, 62, 62, 46, 46, 21, 21, 52, 52, 52, 52, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46] 201 rigid atoms, others: [43, 37, 38, 39, 40, 41, 42, 11, 44, 45, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 362 number of broken/clashed sets: 17 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517661 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517661 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517661/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517661 Building REAL300004517662 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517662' /scratch/stefan/7774842/working/building/REAL300004517662 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517662 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517662/0 /scratch/stefan/7774842/working/building/REAL300004517662 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 702) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/702 `/scratch/stefan/7774842/working/3D/702' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=COC(C=CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=C1) `REAL300004517662.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517662.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517662/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517662 none O=C([O-])C1=COC(C=CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 12, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [198, 198, 198, 198, 198, 198, 172, 172, 74, 40, 74, 8, 1, 1, 1, 1, 1, 1, 1, 1, 40, 52, 52, 52, 52, 198, 198, 172, 172, 8, 8, 1, 1, 1, 1, 52, 52, 52, 52, 52, 52, 52, 52, 52, 198] 201 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 601 number of broken/clashed sets: 29 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517662 none O=C([O-])C1=COC(C=CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 12, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 33, 33, 60, 122, 198, 198, 198, 198, 198, 198, 60, 76, 76, 76, 76, 1, 1, 7, 7, 122, 122, 198, 198, 198, 198, 76, 76, 76, 76, 76, 76, 76, 76, 76, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 44, 25, 26] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 647 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517662 none O=C([O-])C1=COC(C=CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 12, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 76, 76, 76, 76, 46, 46, 15, 7, 15, 1, 7, 22, 52, 52, 52, 52, 52, 52, 1, 1, 1, 1, 1, 76, 76, 46, 46, 22, 22, 52, 52, 52, 52, 1, 1, 1, 1, 1, 1, 1, 1, 1, 76] 201 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 43, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44]) total number of confs: 273 number of broken/clashed sets: 29 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517662 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517662 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517662/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517662 Building REAL300004517663 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517663' /scratch/stefan/7774842/working/building/REAL300004517663 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517663 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517663/0 /scratch/stefan/7774842/working/building/REAL300004517663 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 703) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/703 `/scratch/stefan/7774842/working/3D/703' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C(COCC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)OC=N1) `REAL300004517663.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517663 none O=C([O-])C1=C(COCC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)OC=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 5, 12, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 201, 201, 201, 161, 83, 32, 19, 19, 19, 7, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 201, 201, 201, 161, 161, 32, 32, 7, 7, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 201] 201 rigid atoms, others: [33, 34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 599 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517663 none O=C([O-])C1=C(COCC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)OC=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 5, 12, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 7, 23, 47, 58, 58, 58, 99, 201, 201, 201, 201, 201, 201, 58, 58, 58, 58, 58, 1, 1, 1, 7, 7, 46, 46, 99, 99, 201, 201, 201, 201, 58, 58, 58, 58, 58, 58, 58, 58, 58, 1] 201 rigid atoms, others: [1, 3, 4, 5, 46, 24, 25, 26] set([0, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 615 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517663 none O=C([O-])C1=C(COCC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)OC=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 5, 12, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 12, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [68, 58, 68, 58, 39, 17, 5, 2, 2, 2, 1, 2, 8, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 58, 58, 58, 39, 39, 5, 5, 8, 8, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 58] 201 rigid atoms, others: [37, 38, 39, 40, 41, 10, 43, 44, 45, 19, 20, 21, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46]) total number of confs: 233 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517663 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517663 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517663/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517663 Building REAL300004517664 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517664' /scratch/stefan/7774842/working/building/REAL300004517664 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517664 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517664/0 /scratch/stefan/7774842/working/building/REAL300004517664 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 704) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/704 `/scratch/stefan/7774842/working/3D/704' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)O1) `REAL300004517664.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517664.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517664/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517664 none O=C([O-])C1=CC=C(C=CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [127, 127, 127, 127, 127, 127, 119, 119, 66, 35, 66, 9, 1, 1, 1, 1, 1, 1, 1, 1, 35, 54, 54, 54, 54, 127, 127, 127, 119, 119, 9, 9, 1, 1, 1, 1, 54, 54, 54, 54, 54, 54, 54, 54, 54] 135 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 452 number of broken/clashed sets: 77 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517664 none O=C([O-])C1=CC=C(C=CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 5, 5, 22, 22, 40, 71, 127, 127, 127, 127, 127, 127, 40, 61, 61, 61, 61, 1, 1, 1, 5, 5, 71, 71, 127, 127, 127, 127, 61, 61, 61, 61, 61, 61, 61, 61, 61] 135 rigid atoms, others: [1, 3, 4, 5, 6, 7, 25, 26, 27] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 427 number of broken/clashed sets: 77 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517664 none O=C([O-])C1=CC=C(C=CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 61, 61, 61, 61, 49, 49, 21, 8, 21, 1, 8, 25, 54, 54, 54, 54, 54, 54, 1, 1, 1, 1, 1, 61, 61, 61, 49, 49, 25, 25, 54, 54, 54, 54, 1, 1, 1, 1, 1, 1, 1, 1, 1] 135 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 264 number of broken/clashed sets: 77 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517664 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517664 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517664/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517664 Building REAL300004517665 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517665' /scratch/stefan/7774842/working/building/REAL300004517665 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517665 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517665/0 /scratch/stefan/7774842/working/building/REAL300004517665 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 705) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/705 `/scratch/stefan/7774842/working/3D/705' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])[C@@H]1CC[C@H](C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C1) `REAL300004517665.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517665/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517665 none O=C([O-])[C@@H]1CC[C@H](C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [185, 169, 185, 169, 169, 169, 169, 90, 169, 41, 90, 9, 1, 1, 1, 1, 1, 1, 1, 1, 41, 64, 64, 64, 64, 169, 169, 169, 169, 169, 9, 9, 1, 1, 1, 1, 64, 64, 64, 64, 64, 64, 64, 64, 64, 169, 169] 201 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 658 number of broken/clashed sets: 87 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517665 none O=C([O-])[C@@H]1CC[C@H](C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 25, 70, 169, 169, 169, 169, 169, 169, 25, 43, 43, 43, 43, 1, 1, 1, 1, 1, 70, 70, 169, 169, 169, 169, 43, 43, 43, 43, 43, 43, 43, 43, 43, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 45, 46, 25, 26, 27, 28, 29] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 474 number of broken/clashed sets: 87 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517665 none O=C([O-])[C@@H]1CC[C@H](C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 43, 59, 43, 43, 43, 43, 21, 43, 8, 21, 1, 8, 22, 64, 64, 64, 64, 64, 64, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 22, 22, 64, 64, 64, 64, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43] 201 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 288 number of broken/clashed sets: 87 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517665 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517665 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517665/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517665 Building REAL300004517666 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517666' /scratch/stefan/7774842/working/building/REAL300004517666 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517666 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517666/0 /scratch/stefan/7774842/working/building/REAL300004517666 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 706) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/706 `/scratch/stefan/7774842/working/3D/706' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C1C(=O)[O-]) `REAL300004517666.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517666.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517666/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517666 none CC1=CC=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [180, 180, 180, 180, 84, 40, 84, 9, 1, 1, 1, 1, 1, 1, 1, 1, 40, 61, 61, 61, 61, 180, 180, 180, 189, 189, 180, 180, 180, 180, 180, 9, 9, 1, 1, 1, 1, 61, 61, 61, 61, 61, 61, 61, 61, 61, 180] 201 rigid atoms, others: [33, 34, 35, 36, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 510 number of broken/clashed sets: 17 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517666 none CC1=CC=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 10, 30, 75, 180, 180, 180, 180, 180, 180, 30, 44, 44, 44, 44, 1, 1, 1, 3, 3, 2, 2, 2, 1, 1, 75, 75, 180, 180, 180, 180, 44, 44, 44, 44, 44, 44, 44, 44, 44, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 46, 21, 22, 23, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 486 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517666 none CC1=CC=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [44, 44, 44, 44, 17, 8, 17, 1, 8, 24, 61, 61, 61, 61, 61, 61, 1, 1, 1, 1, 1, 44, 44, 44, 60, 60, 44, 44, 44, 44, 44, 24, 24, 61, 61, 61, 61, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44] 201 rigid atoms, others: [43, 37, 38, 7, 40, 41, 42, 39, 44, 45, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 8, 9, 10, 11, 12, 13, 14, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46]) total number of confs: 258 number of broken/clashed sets: 17 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517666 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517666 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517666/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517666 Building REAL300004517667 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517667' /scratch/stefan/7774842/working/building/REAL300004517667 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517667 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517667/0 /scratch/stefan/7774842/working/building/REAL300004517667 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 707) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/707 `/scratch/stefan/7774842/working/3D/707' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN=CC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=C1) `REAL300004517667.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517667/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517667 none O=C([O-])C1=CN=CC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [174, 174, 174, 174, 174, 174, 174, 101, 41, 101, 9, 1, 1, 1, 1, 1, 1, 1, 1, 41, 69, 69, 69, 69, 174, 174, 174, 9, 9, 1, 1, 1, 1, 69, 69, 69, 69, 69, 69, 69, 69, 69, 174] 187 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 529 number of broken/clashed sets: 26 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517667 none O=C([O-])C1=CN=CC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 28, 84, 174, 174, 174, 174, 174, 174, 28, 51, 51, 51, 51, 1, 1, 1, 84, 84, 174, 174, 174, 174, 51, 51, 51, 51, 51, 51, 51, 51, 51, 1] 187 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 42, 24, 25, 26] set([9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 530 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517667 none O=C([O-])C1=CN=CC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 51, 51, 51, 51, 20, 9, 20, 1, 9, 28, 69, 69, 69, 69, 69, 69, 1, 1, 1, 1, 1, 51, 51, 51, 28, 28, 69, 69, 69, 69, 1, 1, 1, 1, 1, 1, 1, 1, 1, 51] 187 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 10, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42]) total number of confs: 227 number of broken/clashed sets: 26 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517667 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517667 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517667/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517667 Building REAL300004517668 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517668' /scratch/stefan/7774842/working/building/REAL300004517668 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517668 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517668/0 /scratch/stefan/7774842/working/building/REAL300004517668 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 708) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/708 `/scratch/stefan/7774842/working/3D/708' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=NC=C(C(=O)[O-])C=C1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1) `REAL300004517668.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517668.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517668/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517668 none CC1=NC=C(C(=O)[O-])C=C1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [161, 161, 161, 161, 161, 161, 161, 161, 161, 92, 35, 92, 8, 1, 1, 1, 1, 1, 1, 1, 1, 35, 74, 74, 74, 74, 161, 161, 161, 161, 161, 8, 8, 1, 1, 1, 1, 74, 74, 74, 74, 74, 74, 74, 74, 74] 201 rigid atoms, others: [33, 34, 35, 36, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 506 number of broken/clashed sets: 47 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517668 none CC1=NC=C(C(=O)[O-])C=C1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 9, 9, 24, 76, 161, 161, 161, 161, 161, 161, 24, 63, 63, 63, 63, 2, 2, 2, 1, 1, 76, 76, 161, 161, 161, 161, 63, 63, 63, 63, 63, 63, 63, 63, 63] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 8, 9, 10, 29, 30] set([6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 540 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517668 none CC1=NC=C(C(=O)[O-])C=C1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [63, 63, 63, 63, 63, 63, 63, 63, 63, 27, 10, 27, 1, 10, 31, 74, 74, 74, 74, 74, 74, 1, 1, 1, 1, 1, 63, 63, 63, 63, 63, 31, 31, 74, 74, 74, 74, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 44, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 275 number of broken/clashed sets: 47 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517668 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517668 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517668/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517668 Building REAL300004517669 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517669' /scratch/stefan/7774842/working/building/REAL300004517669 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517669 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517669/0 /scratch/stefan/7774842/working/building/REAL300004517669 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 709) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/709 `/scratch/stefan/7774842/working/3D/709' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=NN(CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C1) `REAL300004517669.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517669.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517669/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517669 none O=C([O-])C1=NN(CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [193, 193, 193, 193, 193, 131, 75, 38, 75, 8, 1, 1, 1, 1, 1, 1, 1, 1, 38, 52, 52, 52, 52, 193, 193, 131, 131, 8, 8, 1, 1, 1, 1, 52, 52, 52, 52, 52, 52, 52, 52, 52, 193, 193] 201 rigid atoms, others: [32, 10, 11, 12, 13, 14, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 658 number of broken/clashed sets: 77 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517669 none O=C([O-])C1=NN(CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 9, 20, 20, 47, 106, 193, 193, 193, 193, 193, 193, 47, 68, 68, 68, 68, 1, 1, 9, 9, 106, 106, 193, 193, 193, 193, 68, 68, 68, 68, 68, 68, 68, 68, 68, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 42, 43, 23, 24] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 640 number of broken/clashed sets: 77 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517669 none O=C([O-])C1=NN(CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [68, 68, 68, 68, 68, 38, 16, 6, 16, 1, 6, 20, 52, 52, 52, 52, 52, 52, 1, 1, 1, 1, 1, 68, 68, 38, 38, 20, 20, 52, 52, 52, 52, 1, 1, 1, 1, 1, 1, 1, 1, 1, 68, 68] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 9, 18, 19, 20, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43]) total number of confs: 282 number of broken/clashed sets: 77 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517669 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517669 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517669/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517669 Building REAL300004517670 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517670' /scratch/stefan/7774842/working/building/REAL300004517670 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517670 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517670/0 /scratch/stefan/7774842/working/building/REAL300004517670 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 710) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/710 `/scratch/stefan/7774842/working/3D/710' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=NN(CCCC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C1) `REAL300004517670.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517670.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517670/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517670 none O=C([O-])C1=NN(CCCC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [195, 195, 195, 195, 195, 148, 125, 110, 67, 35, 67, 8, 1, 1, 1, 1, 1, 1, 1, 1, 35, 53, 53, 53, 53, 195, 195, 148, 148, 125, 125, 110, 110, 8, 8, 1, 1, 1, 1, 53, 53, 53, 53, 53, 53, 53, 53, 53, 195, 195] 201 rigid atoms, others: [35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 787 number of broken/clashed sets: 66 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517670 none O=C([O-])C1=NN(CCCC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 7, 9, 15, 28, 28, 56, 110, 195, 195, 195, 195, 195, 195, 56, 78, 78, 78, 78, 1, 1, 7, 7, 9, 9, 15, 15, 110, 110, 195, 195, 195, 195, 78, 78, 78, 78, 78, 78, 78, 78, 78, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 48, 49, 25, 26] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 664 number of broken/clashed sets: 66 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517670 none O=C([O-])C1=NN(CCCC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [78, 78, 78, 78, 78, 54, 46, 39, 16, 7, 16, 1, 7, 22, 53, 53, 53, 53, 53, 53, 1, 1, 1, 1, 1, 78, 78, 54, 54, 46, 46, 39, 39, 22, 22, 53, 53, 53, 53, 1, 1, 1, 1, 1, 1, 1, 1, 1, 78, 78] 201 rigid atoms, others: [43, 39, 40, 41, 42, 11, 44, 45, 46, 47, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 378 number of broken/clashed sets: 66 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517670 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517670 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517670/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517670 Building REAL300004517671 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517671' /scratch/stefan/7774842/working/building/REAL300004517671 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517671 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517671/0 /scratch/stefan/7774842/working/building/REAL300004517671 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 711) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/711 `/scratch/stefan/7774842/working/3D/711' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])[C@@H]1CC[C@@H]1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1) `REAL300004517671.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517671.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517671/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517671 none O=C([O-])[C@@H]1CC[C@@H]1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 35, 34, 35, 25, 34, 9, 1, 1, 1, 1, 1, 1, 1, 1, 25, 30, 30, 30, 30, 35, 35, 35, 35, 9, 9, 1, 1, 1, 1, 30, 30, 30, 30, 30, 30, 30, 30, 30] 36 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 132 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517671 none O=C([O-])[C@@H]1CC[C@@H]1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 17, 35, 35, 35, 35, 35, 35, 9, 11, 11, 11, 11, 1, 1, 1, 1, 17, 17, 35, 35, 35, 35, 11, 11, 11, 11, 11, 11, 11, 11, 11] 36 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 25, 26, 27, 28] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 105 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517671 none O=C([O-])[C@@H]1CC[C@@H]1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [12, 11, 12, 11, 11, 11, 11, 9, 11, 6, 9, 1, 6, 12, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 1, 11, 11, 11, 11, 12, 12, 30, 30, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1] 36 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 43, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 86 number of broken/clashed sets: 14 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517671 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517671 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517671/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517671 Building REAL300004517672 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517672' /scratch/stefan/7774842/working/building/REAL300004517672 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517672 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517672/0 /scratch/stefan/7774842/working/building/REAL300004517672 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 712) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/712 `/scratch/stefan/7774842/working/3D/712' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC[C@@H]1CC[C@H](C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)O1) `REAL300004517672.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517672.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517672/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517672 none O=C([O-])CC[C@@H]1CC[C@H](C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [199, 198, 199, 180, 93, 93, 93, 93, 93, 63, 93, 38, 63, 8, 1, 1, 1, 1, 1, 1, 1, 1, 38, 47, 47, 47, 47, 93, 198, 198, 180, 180, 93, 93, 93, 93, 8, 8, 1, 1, 1, 1, 47, 47, 47, 47, 47, 47, 47, 47, 47] 201 rigid atoms, others: [38, 39, 40, 41, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 871 number of broken/clashed sets: 17 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517672 none O=C([O-])CC[C@@H]1CC[C@H](C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 12, 19, 7, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 14, 40, 93, 93, 93, 93, 93, 93, 14, 24, 24, 24, 24, 1, 12, 12, 7, 7, 1, 1, 1, 1, 40, 40, 93, 93, 93, 93, 24, 24, 24, 24, 24, 24, 24, 24, 24] 201 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 27] set([0, 1, 2, 3, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 335 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517672 none O=C([O-])CC[C@@H]1CC[C@H](C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)O1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [77, 65, 77, 56, 24, 24, 24, 24, 24, 14, 24, 7, 14, 1, 7, 21, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 24, 65, 65, 56, 56, 24, 24, 24, 24, 21, 21, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [42, 43, 44, 13, 46, 45, 48, 49, 50, 22, 23, 24, 25, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 404 number of broken/clashed sets: 17 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517672 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517672 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517672/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517672 Building REAL300004517673 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517673' /scratch/stefan/7774842/working/building/REAL300004517673 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517673 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517673/0 /scratch/stefan/7774842/working/building/REAL300004517673 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 713) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/713 `/scratch/stefan/7774842/working/3D/713' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])[C@@H]1CO[C@H](CCC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C1) `REAL300004517673.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517673.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517673/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517673 none O=C([O-])[C@@H]1CO[C@H](CCC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 12, 5, 7, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [201, 194, 201, 194, 194, 194, 194, 122, 194, 114, 53, 39, 53, 8, 1, 1, 1, 1, 1, 1, 1, 1, 39, 44, 44, 44, 44, 194, 194, 194, 122, 122, 114, 114, 8, 8, 1, 1, 1, 1, 44, 44, 44, 44, 44, 44, 44, 44, 44, 194, 194] 201 rigid atoms, others: [36, 37, 38, 39, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 763 number of broken/clashed sets: 66 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517673 none O=C([O-])[C@@H]1CO[C@H](CCC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 12, 5, 7, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 7, 10, 30, 30, 55, 106, 194, 194, 194, 194, 194, 194, 55, 72, 72, 72, 72, 1, 1, 1, 7, 7, 10, 10, 106, 106, 194, 194, 194, 194, 72, 72, 72, 72, 72, 72, 72, 72, 72, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 49, 50, 27, 28, 29] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 643 number of broken/clashed sets: 66 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517673 none O=C([O-])[C@@H]1CO[C@H](CCC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 12, 5, 7, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [81, 74, 81, 74, 74, 74, 74, 37, 74, 32, 12, 6, 12, 1, 6, 16, 45, 45, 45, 45, 45, 45, 1, 1, 1, 1, 1, 74, 74, 74, 37, 37, 32, 32, 16, 16, 45, 45, 45, 45, 1, 1, 1, 1, 1, 1, 1, 1, 1, 74, 74] 201 rigid atoms, others: [40, 41, 42, 43, 44, 13, 46, 45, 48, 22, 23, 24, 25, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 364 number of broken/clashed sets: 67 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517673 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517673 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517673/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517673 Building REAL300004517674 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517674' /scratch/stefan/7774842/working/building/REAL300004517674 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517674 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517674/0 /scratch/stefan/7774842/working/building/REAL300004517674 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 714) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/714 `/scratch/stefan/7774842/working/3D/714' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])[C@@H]1CC[C@@H]1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1) `REAL300004517674.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517674.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517674/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517674 none O=C([O-])[C@@H]1CC[C@@H]1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [35, 35, 35, 35, 35, 35, 35, 34, 35, 25, 34, 9, 1, 1, 1, 1, 1, 1, 1, 1, 25, 30, 30, 30, 30, 35, 35, 35, 35, 9, 9, 1, 1, 1, 1, 30, 30, 30, 30, 30, 30, 30, 30, 30] 36 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 132 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517674 none O=C([O-])[C@@H]1CC[C@@H]1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 17, 35, 35, 35, 35, 35, 35, 9, 11, 11, 11, 11, 1, 1, 1, 1, 17, 17, 35, 35, 35, 35, 11, 11, 11, 11, 11, 11, 11, 11, 11] 36 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 25, 26, 27, 28] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 105 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517674 none O=C([O-])[C@@H]1CC[C@@H]1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 36 conformations in input total number of sets (complete confs): 36 using default count positions algorithm for smaller data unique positions, atoms: [12, 11, 12, 11, 11, 11, 11, 9, 11, 6, 9, 1, 6, 12, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 1, 11, 11, 11, 11, 12, 12, 30, 30, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1] 36 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 43, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 86 number of broken/clashed sets: 14 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517674 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517674 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517674/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517674 Building REAL300004517675 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517675' /scratch/stefan/7774842/working/building/REAL300004517675 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517675 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517675/0 /scratch/stefan/7774842/working/building/REAL300004517675 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 715) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/715 `/scratch/stefan/7774842/working/3D/715' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])[C@@H]1C[C@@H]1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1) `REAL300004517675.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517675.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517675/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517675 none O=C([O-])[C@@H]1C[C@@H]1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 28, 28, 28, 28, 28, 28, 23, 28, 8, 1, 1, 1, 1, 1, 1, 1, 1, 23, 24, 24, 24, 24, 28, 28, 8, 8, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24] 28 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 91 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517675 none O=C([O-])[C@@H]1C[C@@H]1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 7, 11, 28, 28, 28, 28, 28, 28, 7, 8, 8, 8, 8, 1, 1, 11, 11, 28, 28, 28, 28, 8, 8, 8, 8, 8, 8, 8, 8, 8] 28 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 24, 25] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 73 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517675 none O=C([O-])[C@@H]1C[C@@H]1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [8, 8, 8, 8, 8, 8, 7, 8, 4, 7, 1, 4, 10, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 8, 8, 10, 10, 24, 24, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1] 28 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 10, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 70 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517675 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517675 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517675/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517675 Building REAL300004517676 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517676' /scratch/stefan/7774842/working/building/REAL300004517676 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517676 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517676/0 /scratch/stefan/7774842/working/building/REAL300004517676 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 716) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/716 `/scratch/stefan/7774842/working/3D/716' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)OC(C(=O)[O-])=C1) `REAL300004517676.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517676.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517676/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517676 none CC1=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)OC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 12, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [153, 153, 91, 43, 91, 9, 1, 1, 1, 1, 1, 1, 1, 1, 43, 70, 70, 70, 70, 153, 153, 153, 153, 153, 153, 153, 153, 153, 9, 9, 1, 1, 1, 1, 70, 70, 70, 70, 70, 70, 70, 70, 70, 153] 163 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 451 number of broken/clashed sets: 70 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517676 none CC1=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)OC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 12, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 9, 9, 29, 70, 153, 153, 153, 153, 153, 153, 29, 52, 52, 52, 52, 1, 1, 1, 2, 2, 1, 2, 2, 2, 70, 70, 153, 153, 153, 153, 52, 52, 52, 52, 52, 52, 52, 52, 52, 1] 163 rigid atoms, others: [0, 1, 2, 3, 43, 19, 20, 21, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 472 number of broken/clashed sets: 70 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517676 none CC1=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)OC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 12, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 163 conformations in input total number of sets (complete confs): 163 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 23, 8, 23, 1, 8, 30, 70, 70, 70, 70, 70, 70, 1, 1, 1, 1, 1, 52, 52, 52, 52, 52, 52, 52, 52, 52, 30, 30, 70, 70, 70, 70, 1, 1, 1, 1, 1, 1, 1, 1, 1, 52] 163 rigid atoms, others: [34, 35, 36, 5, 38, 39, 40, 41, 42, 14, 15, 16, 17, 18, 37] set([0, 1, 2, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43]) total number of confs: 242 number of broken/clashed sets: 70 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517676 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517676 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517676/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517676 Building REAL300004517677 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517677' /scratch/stefan/7774842/working/building/REAL300004517677 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517677 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517677/0 /scratch/stefan/7774842/working/building/REAL300004517677 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 717) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/717 `/scratch/stefan/7774842/working/3D/717' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])[C@H]1C2C=CC(CC2)[C@H]1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1) `REAL300004517677.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517677/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517677 none O=C([O-])[C@H]1C2C=CC(CC2)[C@H]1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 1, 1, 5, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 27, 41, 9, 1, 1, 1, 1, 1, 1, 1, 1, 27, 35, 35, 35, 35, 41, 41, 41, 41, 41, 41, 41, 41, 9, 9, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35, 35, 35, 35] 44 rigid atoms, others: [39, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 162 number of broken/clashed sets: 22 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517677 none O=C([O-])[C@H]1C2C=CC(CC2)[C@H]1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 1, 1, 5, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 8, 20, 41, 41, 41, 41, 41, 41, 8, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 41, 41, 41, 41, 16, 16, 16, 16, 16, 16, 16, 16, 16] 44 rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 35, 36, 33, 29, 30, 31] set([0, 2, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 142 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517677 none O=C([O-])[C@H]1C2C=CC(CC2)[C@H]1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 1, 1, 5, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 44 conformations in input total number of sets (complete confs): 44 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 15, 16, 7, 15, 1, 7, 18, 35, 35, 35, 35, 35, 35, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 18, 18, 35, 35, 35, 35, 1, 1, 1, 1, 1, 1, 1, 1, 1] 44 rigid atoms, others: [47, 43, 44, 45, 46, 15, 48, 49, 50, 51, 24, 25, 26, 27, 28] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 125 number of broken/clashed sets: 22 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517677 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517677 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517677/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517677 Building REAL300004517678 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517678' /scratch/stefan/7774842/working/building/REAL300004517678 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517678 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517678/0 /scratch/stefan/7774842/working/building/REAL300004517678 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 718) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/718 `/scratch/stefan/7774842/working/3D/718' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C(=O)[O-])C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1) `REAL300004517678.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517678.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517678/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517678 none CCC(C(=O)[O-])C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 11, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [39, 27, 15, 27, 34, 34, 7, 15, 1, 7, 20, 63, 63, 63, 63, 63, 63, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 27, 20, 20, 63, 63, 63, 63, 1, 1, 1, 1, 1, 1, 1, 1, 1] 138 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 41, 42, 17, 18, 19, 20, 21, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 309 number of broken/clashed sets: 48 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517678 none CCC(C(=O)[O-])C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 11, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 138 conformations in input total number of sets (complete confs): 138 using faster count positions algorithm for large data unique positions, atoms: [126, 101, 75, 101, 118, 118, 40, 75, 8, 1, 1, 1, 1, 1, 1, 1, 1, 40, 63, 63, 63, 63, 126, 126, 126, 126, 126, 101, 8, 8, 1, 1, 1, 1, 63, 63, 63, 63, 63, 63, 63, 63, 63] 138 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 666 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517678 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517678 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517678/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517678 Building REAL300004517679 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517679' /scratch/stefan/7774842/working/building/REAL300004517679 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517679 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517679/0 /scratch/stefan/7774842/working/building/REAL300004517679 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 719) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/719 `/scratch/stefan/7774842/working/3D/719' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C(C(=O)[O-])C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1) `REAL300004517679.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517679.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517679/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517679 none CC(C)C(C(=O)[O-])C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [26, 22, 26, 14, 22, 22, 22, 7, 14, 1, 7, 20, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 26, 26, 22, 20, 20, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 68 rigid atoms, others: [37, 38, 39, 40, 9, 42, 43, 44, 45, 18, 19, 20, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 199 number of broken/clashed sets: 24 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517679 none CC(C)C(C(=O)[O-])C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [64, 63, 64, 60, 63, 63, 63, 37, 60, 8, 1, 1, 1, 1, 1, 1, 1, 1, 37, 50, 50, 50, 50, 64, 64, 64, 64, 64, 64, 64, 63, 8, 8, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50] 68 rigid atoms, others: [33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 257 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517679 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517679 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517679/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517679 Building REAL300004517680 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517680' /scratch/stefan/7774842/working/building/REAL300004517680 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517680 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517680/0 /scratch/stefan/7774842/working/building/REAL300004517680 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 720) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/720 `/scratch/stefan/7774842/working/3D/720' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])[C@@H]1CCCC[C@@H]1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1) `REAL300004517680.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517680.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517680/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517680 none O=C([O-])[C@@H]1CCCC[C@@H]1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [57, 57, 57, 57, 57, 57, 57, 57, 57, 49, 57, 35, 49, 9, 1, 1, 1, 1, 1, 1, 1, 1, 35, 36, 36, 36, 36, 57, 57, 57, 57, 57, 57, 57, 57, 9, 9, 1, 1, 1, 1, 36, 36, 36, 36, 36, 36, 36, 36, 36] 57 rigid atoms, others: [37, 38, 39, 40, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 168 number of broken/clashed sets: 34 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517680 none O=C([O-])[C@@H]1CCCC[C@@H]1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 12, 28, 57, 57, 57, 57, 57, 57, 12, 15, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 57, 57, 57, 57, 15, 15, 15, 15, 15, 15, 15, 15, 15] 57 rigid atoms, others: [32, 1, 34, 3, 4, 5, 6, 7, 8, 9, 10, 11, 33, 27, 28, 29, 30, 31] set([0, 2, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 169 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517680 none O=C([O-])[C@@H]1CCCC[C@@H]1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 5, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [16, 15, 16, 15, 15, 15, 15, 15, 15, 11, 15, 4, 11, 1, 4, 14, 36, 36, 36, 36, 36, 36, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 14, 14, 36, 36, 36, 36, 1, 1, 1, 1, 1, 1, 1, 1, 1] 57 rigid atoms, others: [41, 42, 43, 44, 13, 46, 45, 48, 49, 22, 23, 24, 25, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 117 number of broken/clashed sets: 34 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517680 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517680 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517680/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517680 Building REAL300004517681 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517681' /scratch/stefan/7774842/working/building/REAL300004517681 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004517681 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517681/0 /scratch/stefan/7774842/working/building/REAL300004517681 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 721) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/721 `/scratch/stefan/7774842/working/3D/721' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1CCC[N@H+](CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C1) `REAL300004517681.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517681/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517681 none O=C([O-])C1CCC[N@H+](CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [55, 51, 55, 51, 51, 51, 51, 51, 51, 46, 31, 46, 9, 1, 1, 1, 1, 1, 1, 1, 1, 31, 40, 40, 40, 40, 51, 51, 51, 51, 51, 51, 51, 51, 51, 51, 9, 9, 1, 1, 1, 1, 40, 40, 40, 40, 40, 40, 40, 40, 40, 51, 51] 59 rigid atoms, others: [38, 39, 40, 41, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 214 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517681 none O=C([O-])C1CCC[N@H+](CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 8, 8, 16, 27, 51, 51, 51, 51, 51, 51, 16, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 27, 27, 51, 51, 51, 51, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1] 59 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 33, 51, 52, 26, 27, 28, 29, 30, 31] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 162 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517681 none O=C([O-])C1CCC[N@H+](CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [23, 19, 23, 19, 19, 19, 19, 15, 19, 10, 4, 10, 1, 4, 15, 40, 40, 40, 40, 40, 40, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 15, 15, 15, 15, 40, 40, 40, 40, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19] 59 rigid atoms, others: [44, 42, 43, 12, 45, 46, 47, 48, 49, 50, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 163 number of broken/clashed sets: 16 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517681 /scratch/stefan/7774842/working /scratch/stefan/7774842 mkdir: created directory `1' /scratch/stefan/7774842/working/building/REAL300004517681/1 /scratch/stefan/7774842/working/building/REAL300004517681 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 1 (index: 722) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/722 `/scratch/stefan/7774842/working/3D/722' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1CCC[N@@H+](CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C1) `REAL300004517681.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004517681.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517681/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517681 none O=C([O-])C1CCC[N@@H+](CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [57, 55, 57, 55, 55, 55, 55, 52, 55, 31, 25, 31, 8, 1, 1, 1, 1, 1, 1, 1, 1, 25, 31, 31, 31, 31, 55, 55, 55, 55, 55, 55, 55, 55, 52, 52, 8, 8, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 31, 31, 31, 55, 55] 61 rigid atoms, others: [38, 39, 40, 41, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 245 number of broken/clashed sets: 22 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517681 none O=C([O-])C1CCC[N@@H+](CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 5, 13, 13, 19, 29, 55, 55, 55, 55, 55, 55, 19, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 29, 29, 55, 55, 55, 55, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1] 61 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 33, 51, 52, 26, 27, 28, 29, 30, 31] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 174 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517681 none O=C([O-])C1CCC[N@@H+](CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 9, 6, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 1, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [26, 23, 26, 23, 23, 23, 23, 19, 23, 10, 5, 10, 1, 5, 11, 31, 31, 31, 31, 31, 31, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 19, 19, 11, 11, 31, 31, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23] 61 rigid atoms, others: [44, 42, 43, 12, 45, 46, 47, 48, 49, 50, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 147 number of broken/clashed sets: 22 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517681 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517681 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 1: /scratch/stefan/7774842/working/building/REAL300004517681/1.* 0: /scratch/stefan/7774842/working/building/REAL300004517681/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517681 Building REAL300004517682 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517682' /scratch/stefan/7774842/working/building/REAL300004517682 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517682 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517682/0 /scratch/stefan/7774842/working/building/REAL300004517682 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 723) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/723 `/scratch/stefan/7774842/working/3D/723' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])[C@@H]1C[C@H]1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1) `REAL300004517682.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517682/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517682 none O=C([O-])[C@@H]1C[C@H]1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [137, 123, 137, 123, 123, 123, 81, 123, 37, 81, 9, 1, 1, 1, 1, 1, 1, 1, 1, 37, 53, 53, 53, 53, 123, 123, 9, 9, 1, 1, 1, 1, 53, 53, 53, 53, 53, 53, 53, 53, 53] 139 rigid atoms, others: [11, 12, 13, 14, 15, 16, 17, 18, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 512 number of broken/clashed sets: 25 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517682 none O=C([O-])[C@@H]1C[C@H]1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 8, 8, 23, 50, 123, 123, 123, 123, 123, 123, 23, 36, 36, 36, 36, 1, 1, 50, 50, 123, 123, 123, 123, 36, 36, 36, 36, 36, 36, 36, 36, 36] 139 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 24, 25] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 343 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517682 none O=C([O-])[C@@H]1C[C@H]1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [46, 36, 46, 36, 36, 36, 16, 36, 6, 16, 1, 6, 18, 53, 53, 53, 53, 53, 53, 1, 1, 1, 1, 1, 36, 36, 18, 18, 53, 53, 53, 53, 1, 1, 1, 1, 1, 1, 1, 1, 1] 139 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 10, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 235 number of broken/clashed sets: 25 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517682 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517682 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517682/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517682 Building REAL300004517683 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517683' /scratch/stefan/7774842/working/building/REAL300004517683 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517683 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517683/0 /scratch/stefan/7774842/working/building/REAL300004517683 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 724) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/724 `/scratch/stefan/7774842/working/3D/724' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)NC2=CC=CC=C21) `REAL300004517683.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517683.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517683/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517683 none O=C([O-])CC1=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)NC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [84, 82, 84, 82, 82, 61, 37, 61, 9, 1, 1, 1, 1, 1, 1, 1, 1, 37, 49, 49, 49, 49, 82, 82, 82, 82, 82, 82, 82, 82, 82, 9, 9, 1, 1, 1, 1, 49, 49, 49, 49, 49, 49, 49, 49, 49, 82, 82, 82, 82, 82] 90 rigid atoms, others: [33, 34, 35, 36, 9, 10, 11, 12, 13, 14, 15, 16] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 280 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517683 none O=C([O-])CC1=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)NC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [7, 2, 7, 1, 1, 1, 1, 7, 7, 17, 38, 82, 82, 82, 82, 82, 82, 17, 25, 25, 25, 25, 1, 1, 1, 1, 1, 1, 1, 2, 2, 38, 38, 82, 82, 82, 82, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1, 1, 1] 90 rigid atoms, others: [3, 4, 5, 6, 46, 47, 48, 49, 50, 22, 23, 24, 25, 26, 27, 28] set([0, 1, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 264 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517683 none O=C([O-])CC1=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)NC2=CC=CC=C21 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 8, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [30, 25, 30, 25, 25, 13, 7, 13, 1, 7, 19, 49, 49, 49, 49, 49, 49, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 25, 25, 25, 19, 19, 49, 49, 49, 49, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25] 90 rigid atoms, others: [37, 38, 39, 8, 41, 42, 43, 44, 45, 17, 18, 19, 20, 21, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 160 number of broken/clashed sets: 9 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517683 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517683 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517683/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517683 Building REAL300004517684 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517684' /scratch/stefan/7774842/working/building/REAL300004517684 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517684 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517684/0 /scratch/stefan/7774842/working/building/REAL300004517684 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 725) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/725 `/scratch/stefan/7774842/working/3D/725' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CN(CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C2=CC=CC=C12) `REAL300004517684.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517684/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517684 none O=C([O-])C1=CN(CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C2=CC=CC=C12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [122, 122, 122, 122, 122, 86, 41, 23, 41, 7, 1, 1, 1, 1, 1, 1, 1, 1, 23, 28, 28, 28, 28, 122, 122, 122, 122, 122, 122, 122, 86, 86, 7, 7, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28, 28, 122, 122, 122, 122] 123 rigid atoms, others: [34, 35, 36, 37, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 415 number of broken/clashed sets: 53 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517684 none O=C([O-])C1=CN(CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C2=CC=CC=C12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 8, 19, 19, 44, 79, 122, 122, 122, 122, 122, 122, 44, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 8, 8, 79, 79, 122, 122, 122, 122, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1] 123 rigid atoms, others: [1, 3, 4, 5, 6, 47, 48, 49, 50, 23, 24, 25, 26, 27, 28, 29] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 427 number of broken/clashed sets: 53 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517684 none O=C([O-])C1=CN(CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C2=CC=CC=C12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 8, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 123 conformations in input total number of sets (complete confs): 123 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 32, 12, 5, 12, 1, 5, 15, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 32, 32, 15, 15, 28, 28, 28, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 123 rigid atoms, others: [38, 39, 40, 9, 42, 43, 44, 45, 46, 18, 19, 20, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 208 number of broken/clashed sets: 53 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517684 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517684 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517684/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517684 Building REAL300004517685 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517685' /scratch/stefan/7774842/working/building/REAL300004517685 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517685 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517685/0 /scratch/stefan/7774842/working/building/REAL300004517685 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 726) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/726 `/scratch/stefan/7774842/working/3D/726' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1CC12CC(C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1)C2) `REAL300004517685.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517685.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517685/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517685 none O=C([O-])C1CC12CC(C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1)C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [194, 184, 194, 184, 184, 184, 184, 85, 40, 85, 9, 1, 1, 1, 1, 1, 1, 1, 1, 40, 62, 62, 62, 62, 184, 184, 184, 184, 184, 184, 184, 9, 9, 1, 1, 1, 1, 62, 62, 62, 62, 62, 62, 62, 62, 62, 184, 184] 201 rigid atoms, others: [33, 34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 686 number of broken/clashed sets: 48 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517685 none O=C([O-])C1CC12CC(C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1)C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 8, 8, 30, 78, 184, 184, 184, 184, 184, 184, 30, 46, 46, 46, 46, 1, 1, 1, 1, 1, 1, 1, 78, 78, 184, 184, 184, 184, 46, 46, 46, 46, 46, 46, 46, 46, 46, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 46, 47, 24, 25, 26, 27, 28, 29, 30] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 503 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517685 none O=C([O-])C1CC12CC(C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1)C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [63, 46, 63, 46, 46, 46, 46, 18, 7, 18, 1, 7, 22, 62, 62, 62, 62, 62, 62, 1, 1, 1, 1, 1, 46, 46, 46, 46, 46, 46, 46, 22, 22, 62, 62, 62, 62, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46] 201 rigid atoms, others: [37, 38, 39, 40, 41, 10, 43, 44, 45, 19, 20, 21, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 304 number of broken/clashed sets: 48 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517685 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517685 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517685/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517685 Building REAL300004517686 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517686' /scratch/stefan/7774842/working/building/REAL300004517686 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517686 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517686/0 /scratch/stefan/7774842/working/building/REAL300004517686 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 727) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/727 `/scratch/stefan/7774842/working/3D/727' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])[C@H]1C[C@@H](C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C1) `REAL300004517686.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517686/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517686 none O=C([O-])[C@H]1C[C@@H](C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [185, 173, 185, 173, 173, 173, 84, 173, 40, 84, 9, 1, 1, 1, 1, 1, 1, 1, 1, 40, 64, 64, 64, 64, 173, 173, 173, 9, 9, 1, 1, 1, 1, 64, 64, 64, 64, 64, 64, 64, 64, 64, 173, 173] 201 rigid atoms, others: [32, 11, 12, 13, 14, 15, 16, 17, 18, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 660 number of broken/clashed sets: 35 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517686 none O=C([O-])[C@H]1C[C@@H](C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 8, 8, 28, 77, 173, 173, 173, 173, 173, 173, 28, 47, 47, 47, 47, 1, 1, 1, 77, 77, 173, 173, 173, 173, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 42, 43, 24, 25, 26] set([0, 2, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 493 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517686 none O=C([O-])[C@H]1C[C@@H](C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [66, 47, 66, 47, 47, 47, 17, 47, 8, 17, 1, 8, 23, 64, 64, 64, 64, 64, 64, 1, 1, 1, 1, 1, 47, 47, 47, 23, 23, 64, 64, 64, 64, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47] 201 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 10, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43]) total number of confs: 316 number of broken/clashed sets: 35 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517686 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517686 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517686/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517686 Building REAL300004517687 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517687' /scratch/stefan/7774842/working/building/REAL300004517687 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517687 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517687/0 /scratch/stefan/7774842/working/building/REAL300004517687 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 728) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/728 `/scratch/stefan/7774842/working/3D/728' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@]1(C(=O)[O-])C[C@@H]1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1) `REAL300004517687.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517687/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517687 none CC(C)[C@@]1(C(=O)[O-])C[C@@H]1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [13, 13, 13, 13, 13, 13, 13, 13, 11, 13, 8, 11, 7, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 13, 13, 13, 13, 13, 13, 13, 13, 13, 7, 7, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8] 13 rigid atoms, others: [37, 38, 39, 40, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 44 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517687 none CC(C)[C@@]1(C(=O)[O-])C[C@@H]1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [2, 1, 2, 1, 1, 2, 2, 1, 1, 1, 1, 4, 4, 6, 9, 13, 13, 13, 13, 13, 13, 6, 6, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 1, 1, 9, 9, 13, 13, 13, 13, 6, 6, 6, 6, 6, 6, 6, 6, 6] 13 rigid atoms, others: [1, 34, 3, 4, 33, 8, 9, 10, 7] set([0, 2, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 51 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517687 none CC(C)[C@@]1(C(=O)[O-])C[C@@H]1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 5, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [6, 6, 6, 6, 6, 6, 6, 6, 4, 6, 3, 4, 1, 3, 5, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1] 13 rigid atoms, others: [41, 42, 43, 12, 45, 46, 44, 48, 49, 21, 22, 23, 24, 25, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 35 number of broken/clashed sets: 6 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517687 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517687 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517687/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517687 Building REAL300004517688 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517688' /scratch/stefan/7774842/working/building/REAL300004517688 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517688 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517688/0 /scratch/stefan/7774842/working/building/REAL300004517688 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 729) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/729 `/scratch/stefan/7774842/working/3D/729' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(C(=O)[O-])C=C1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1) `REAL300004517688.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517688/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517688 none CC1=CC=C(C(=O)[O-])C=C1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [163, 163, 163, 163, 163, 163, 163, 163, 163, 91, 35, 91, 8, 1, 1, 1, 1, 1, 1, 1, 1, 35, 73, 73, 73, 73, 163, 163, 163, 163, 163, 163, 8, 8, 1, 1, 1, 1, 73, 73, 73, 73, 73, 73, 73, 73, 73] 201 rigid atoms, others: [34, 35, 36, 37, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 502 number of broken/clashed sets: 47 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517688 none CC1=CC=C(C(=O)[O-])C=C1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 9, 9, 24, 78, 163, 163, 163, 163, 163, 163, 24, 61, 61, 61, 61, 2, 2, 2, 1, 1, 1, 78, 78, 163, 163, 163, 163, 61, 61, 61, 61, 61, 61, 61, 61, 61] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 8, 9, 10, 29, 30, 31] set([6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 543 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517688 none CC1=CC=C(C(=O)[O-])C=C1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [61, 61, 61, 61, 61, 61, 61, 61, 61, 27, 10, 27, 1, 10, 32, 73, 73, 73, 73, 73, 73, 1, 1, 1, 1, 1, 61, 61, 61, 61, 61, 61, 32, 32, 73, 73, 73, 73, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [38, 39, 40, 41, 42, 43, 12, 45, 46, 44, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 275 number of broken/clashed sets: 47 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517688 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517688 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517688/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517688 Building REAL300004517689 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517689' /scratch/stefan/7774842/working/building/REAL300004517689 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517689 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517689/0 /scratch/stefan/7774842/working/building/REAL300004517689 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 730) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/730 `/scratch/stefan/7774842/working/3D/730' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C(=O)[O-])CC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C1) `REAL300004517689.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517689/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517689 none CC1(C(=O)[O-])CC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 11, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 2, 2, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [156, 156, 156, 174, 174, 156, 80, 39, 80, 9, 1, 1, 1, 1, 1, 1, 1, 1, 39, 60, 60, 60, 60, 156, 156, 156, 156, 156, 156, 156, 9, 9, 1, 1, 1, 1, 60, 60, 60, 60, 60, 60, 60, 60, 60, 156, 156] 182 rigid atoms, others: [32, 33, 34, 35, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 606 number of broken/clashed sets: 79 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517689 none CC1(C(=O)[O-])CC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 11, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 2, 2, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 3, 3, 1, 1, 1, 8, 8, 27, 66, 156, 156, 156, 156, 156, 156, 27, 50, 50, 50, 50, 1, 2, 2, 2, 1, 1, 1, 66, 66, 156, 156, 156, 156, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1] 182 rigid atoms, others: [0, 1, 2, 5, 6, 7, 45, 46, 23, 27, 28, 29] set([3, 4, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 484 number of broken/clashed sets: 79 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517689 none CC1(C(=O)[O-])CC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 11, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 2, 2, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 182 conformations in input total number of sets (complete confs): 182 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 64, 64, 50, 19, 6, 19, 1, 6, 23, 60, 60, 60, 60, 60, 60, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 23, 23, 60, 60, 60, 60, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 182 rigid atoms, others: [36, 37, 38, 39, 40, 9, 42, 43, 44, 18, 19, 20, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 316 number of broken/clashed sets: 79 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517689 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517689 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517689/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517689 Building REAL300004517690 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517690' /scratch/stefan/7774842/working/building/REAL300004517690 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517690 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517690/0 /scratch/stefan/7774842/working/building/REAL300004517690 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 731) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/731 `/scratch/stefan/7774842/working/3D/731' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=NNC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=C1) `REAL300004517690.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517690.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517690/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517690 none O=C([O-])C1=NNC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [162, 162, 162, 162, 162, 160, 83, 41, 83, 9, 1, 1, 1, 1, 1, 1, 1, 1, 41, 58, 58, 58, 58, 162, 162, 9, 9, 1, 1, 1, 1, 58, 58, 58, 58, 58, 58, 58, 58, 58, 162] 171 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 450 number of broken/clashed sets: 17 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517690 none O=C([O-])C1=NNC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 35, 90, 162, 162, 162, 162, 162, 162, 35, 50, 50, 50, 50, 1, 1, 90, 90, 162, 162, 162, 162, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1] 171 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 40, 23, 24] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 514 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517690 none O=C([O-])C1=NNC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 171 conformations in input total number of sets (complete confs): 171 using faster count positions algorithm for large data unique positions, atoms: [50, 50, 50, 50, 50, 50, 17, 8, 17, 1, 8, 22, 58, 58, 58, 58, 58, 58, 1, 1, 1, 1, 1, 50, 50, 22, 22, 58, 58, 58, 58, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 171 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 9, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 40]) total number of confs: 190 number of broken/clashed sets: 17 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517690 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517690 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517690/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517690 Building REAL300004517691 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517691' /scratch/stefan/7774842/working/building/REAL300004517691 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517691 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517691/0 /scratch/stefan/7774842/working/building/REAL300004517691 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 732) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/732 `/scratch/stefan/7774842/working/3D/732' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=NC=C1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1) `REAL300004517691.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517691.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517691/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517691 none CC1=C(C(=O)[O-])C=NC=C1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 8, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 107, 107, 107, 107, 107, 107, 78, 38, 78, 8, 1, 1, 1, 1, 1, 1, 1, 1, 38, 52, 52, 52, 52, 107, 107, 107, 107, 107, 8, 8, 1, 1, 1, 1, 52, 52, 52, 52, 52, 52, 52, 52, 52] 111 rigid atoms, others: [33, 34, 35, 36, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 348 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517691 none CC1=C(C(=O)[O-])C=NC=C1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 8, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 7, 7, 20, 54, 107, 107, 107, 107, 107, 107, 20, 30, 30, 30, 30, 2, 2, 2, 1, 1, 54, 54, 107, 107, 107, 107, 30, 30, 30, 30, 30, 30, 30, 30, 30] 111 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 9, 10, 29, 30] set([4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 332 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517691 none CC1=C(C(=O)[O-])C=NC=C1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 8, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 111 conformations in input total number of sets (complete confs): 111 using faster count positions algorithm for large data unique positions, atoms: [30, 30, 30, 30, 30, 30, 30, 30, 30, 16, 7, 16, 1, 7, 22, 52, 52, 52, 52, 52, 52, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 22, 22, 52, 52, 52, 52, 1, 1, 1, 1, 1, 1, 1, 1, 1] 111 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 44, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 168 number of broken/clashed sets: 10 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517691 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517691 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517691/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517691 Building REAL300004517692 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517692' /scratch/stefan/7774842/working/building/REAL300004517692 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517692 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517692/0 /scratch/stefan/7774842/working/building/REAL300004517692 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 733) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/733 `/scratch/stefan/7774842/working/3D/733' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C(=O)[O-])C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1) `REAL300004517692.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517692/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517692 none CCCC(C(=O)[O-])C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [50, 48, 27, 12, 27, 34, 34, 6, 12, 1, 6, 17, 42, 42, 42, 42, 42, 42, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 48, 48, 27, 17, 17, 42, 42, 42, 42, 1, 1, 1, 1, 1, 1, 1, 1, 1] 120 rigid atoms, others: [37, 38, 39, 40, 9, 42, 43, 44, 45, 18, 19, 20, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 322 number of broken/clashed sets: 71 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517692 none CCCC(C(=O)[O-])C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [115, 115, 84, 52, 84, 98, 98, 32, 52, 9, 1, 1, 1, 1, 1, 1, 1, 1, 32, 42, 42, 42, 42, 115, 115, 115, 115, 115, 115, 115, 84, 9, 9, 1, 1, 1, 1, 42, 42, 42, 42, 42, 42, 42, 42, 42] 120 rigid atoms, others: [33, 34, 35, 36, 10, 11, 12, 13, 14, 15, 16, 17] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 568 number of broken/clashed sets: 71 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517692 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517692 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517692/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517692 Building REAL300004517693 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517693' /scratch/stefan/7774842/working/building/REAL300004517693 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517693 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517693/0 /scratch/stefan/7774842/working/building/REAL300004517693 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 734) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/734 `/scratch/stefan/7774842/working/3D/734' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1) `REAL300004517693.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517693/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517693 none CC1=CC(C(=O)[O-])=CC=C1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [103, 103, 103, 84, 103, 103, 103, 103, 103, 75, 39, 75, 8, 1, 1, 1, 1, 1, 1, 1, 1, 39, 51, 51, 51, 51, 103, 103, 103, 103, 103, 103, 8, 8, 1, 1, 1, 1, 51, 51, 51, 51, 51, 51, 51, 51, 51] 110 rigid atoms, others: [34, 35, 36, 37, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 422 number of broken/clashed sets: 13 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517693 none CC1=CC(C(=O)[O-])=CC=C1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 8, 8, 20, 52, 103, 103, 103, 103, 103, 103, 20, 31, 31, 31, 31, 2, 2, 2, 1, 1, 1, 52, 52, 103, 103, 103, 103, 31, 31, 31, 31, 31, 31, 31, 31, 31] 110 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 29, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 321 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517693 none CC1=CC(C(=O)[O-])=CC=C1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [31, 31, 31, 17, 24, 31, 31, 31, 31, 17, 8, 17, 1, 8, 21, 51, 51, 51, 51, 51, 51, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 31, 21, 21, 51, 51, 51, 51, 1, 1, 1, 1, 1, 1, 1, 1, 1] 110 rigid atoms, others: [38, 39, 40, 41, 42, 43, 12, 45, 46, 44, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 231 number of broken/clashed sets: 13 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517693 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517693 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517693/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517693 Building REAL300004517694 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517694' /scratch/stefan/7774842/working/building/REAL300004517694 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517694 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517694/0 /scratch/stefan/7774842/working/building/REAL300004517694 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 735) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/735 `/scratch/stefan/7774842/working/3D/735' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C(Cl)=C1) `REAL300004517694.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517694.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517694/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517694 none O=C([O-])C1=CC=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [151, 151, 151, 147, 151, 151, 94, 35, 94, 8, 1, 1, 1, 1, 1, 1, 1, 1, 35, 70, 70, 70, 70, 151, 151, 151, 151, 151, 8, 8, 1, 1, 1, 1, 70, 70, 70, 70, 70, 70, 70, 70, 70, 151] 195 rigid atoms, others: [32, 33, 10, 11, 12, 13, 14, 15, 16, 17, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 505 number of broken/clashed sets: 49 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517694 none O=C([O-])C1=CC=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 23, 70, 151, 151, 151, 151, 151, 151, 23, 58, 58, 58, 58, 1, 1, 1, 1, 1, 70, 70, 151, 151, 151, 151, 58, 58, 58, 58, 58, 58, 58, 58, 58, 1] 195 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 43, 23, 24, 25, 26, 27] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 498 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517694 none O=C([O-])C1=CC=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C(Cl)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'Cl', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 16, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 195 conformations in input total number of sets (complete confs): 195 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 58, 47, 58, 58, 29, 10, 29, 1, 10, 27, 70, 70, 70, 70, 70, 70, 1, 1, 1, 1, 1, 58, 58, 58, 58, 58, 27, 27, 70, 70, 70, 70, 1, 1, 1, 1, 1, 1, 1, 1, 1, 58] 195 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 9, 42, 18, 19, 20, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43]) total number of confs: 314 number of broken/clashed sets: 49 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517694 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517694 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517694/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517694 Building REAL300004517695 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517695' /scratch/stefan/7774842/working/building/REAL300004517695 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517695 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517695/0 /scratch/stefan/7774842/working/building/REAL300004517695 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 736) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/736 `/scratch/stefan/7774842/working/3D/736' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1CC2(C1)CC(C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1)C2) `REAL300004517695.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517695/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517695 none O=C([O-])C1CC2(C1)CC(C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1)C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [184, 175, 184, 175, 175, 175, 175, 175, 96, 40, 96, 9, 1, 1, 1, 1, 1, 1, 1, 1, 40, 67, 67, 67, 67, 175, 175, 175, 175, 175, 175, 175, 175, 175, 9, 9, 1, 1, 1, 1, 67, 67, 67, 67, 67, 67, 67, 67, 67, 175, 175] 201 rigid atoms, others: [36, 37, 38, 39, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 700 number of broken/clashed sets: 47 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517695 none O=C([O-])C1CC2(C1)CC(C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1)C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 8, 8, 28, 70, 175, 175, 175, 175, 175, 175, 28, 49, 49, 49, 49, 1, 1, 1, 1, 1, 1, 1, 1, 1, 70, 70, 175, 175, 175, 175, 49, 49, 49, 49, 49, 49, 49, 49, 49, 1, 1] 201 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 33, 49, 50, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 484 number of broken/clashed sets: 47 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517695 none O=C([O-])C1CC2(C1)CC(C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1)C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [70, 49, 70, 49, 49, 49, 49, 49, 19, 8, 19, 1, 8, 24, 67, 67, 67, 67, 67, 67, 1, 1, 1, 1, 1, 49, 49, 49, 49, 49, 49, 49, 49, 49, 24, 24, 67, 67, 67, 67, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49] 201 rigid atoms, others: [43, 40, 41, 42, 11, 44, 45, 46, 47, 48, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 340 number of broken/clashed sets: 47 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517695 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517695 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517695/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517695 Building REAL300004517696 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517696' /scratch/stefan/7774842/working/building/REAL300004517696 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517696 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517696/0 /scratch/stefan/7774842/working/building/REAL300004517696 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 737) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/737 `/scratch/stefan/7774842/working/3D/737' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)[O-])=NC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=C1) `REAL300004517696.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517696/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517696 none COC1=CC(C(=O)[O-])=NC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [182, 171, 171, 171, 171, 171, 171, 171, 171, 95, 44, 95, 9, 1, 1, 1, 1, 1, 1, 1, 1, 44, 67, 67, 67, 67, 171, 182, 182, 182, 171, 9, 9, 1, 1, 1, 1, 67, 67, 67, 67, 67, 67, 67, 67, 67, 171] 198 rigid atoms, others: [33, 34, 35, 36, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 512 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517696 none COC1=CC(C(=O)[O-])=NC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 8, 8, 28, 71, 171, 171, 171, 171, 171, 171, 28, 45, 45, 45, 45, 1, 3, 3, 3, 1, 71, 71, 171, 171, 171, 171, 45, 45, 45, 45, 45, 45, 45, 45, 45, 1] 198 rigid atoms, others: [1, 2, 3, 4, 5, 8, 9, 10, 46, 26, 30] set([0, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 472 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517696 none COC1=CC(C(=O)[O-])=NC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 198 conformations in input total number of sets (complete confs): 198 using faster count positions algorithm for large data unique positions, atoms: [56, 45, 45, 45, 45, 45, 45, 45, 45, 18, 8, 18, 1, 8, 25, 67, 67, 67, 67, 67, 67, 1, 1, 1, 1, 1, 45, 56, 56, 56, 45, 25, 25, 67, 67, 67, 67, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45] 198 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 44, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46]) total number of confs: 229 number of broken/clashed sets: 14 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517696 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517696 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517696/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517696 Building REAL300004517697 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517697' /scratch/stefan/7774842/working/building/REAL300004517697 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517697 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517697/0 /scratch/stefan/7774842/working/building/REAL300004517697 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 738) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/738 `/scratch/stefan/7774842/working/3D/738' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(C(=O)[O-])=CC=C1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1) `REAL300004517697.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517697/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517697 none CN1C(C(=O)[O-])=CC=C1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 11, 11, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [164, 164, 164, 164, 164, 164, 164, 164, 94, 35, 94, 8, 1, 1, 1, 1, 1, 1, 1, 1, 35, 78, 78, 78, 78, 164, 164, 164, 164, 164, 8, 8, 1, 1, 1, 1, 78, 78, 78, 78, 78, 78, 78, 78, 78] 201 rigid atoms, others: [32, 33, 34, 35, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 537 number of broken/clashed sets: 19 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517697 none CN1C(C(=O)[O-])=CC=C1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 11, 11, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 9, 9, 28, 71, 164, 164, 164, 164, 164, 164, 28, 71, 71, 71, 71, 2, 2, 2, 1, 1, 71, 71, 164, 164, 164, 164, 71, 71, 71, 71, 71, 71, 71, 71, 71] 201 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 9, 28, 29] set([4, 5, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 543 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517697 none CN1C(C(=O)[O-])=CC=C1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 11, 11, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 71, 71, 71, 71, 71, 29, 11, 29, 1, 11, 30, 78, 78, 78, 78, 78, 78, 1, 1, 1, 1, 1, 71, 71, 71, 71, 71, 30, 30, 78, 78, 78, 78, 1, 1, 1, 1, 1, 1, 1, 1, 1] 201 rigid atoms, others: [43, 36, 37, 38, 39, 40, 41, 42, 11, 44, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 291 number of broken/clashed sets: 19 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517697 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517697 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517697/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517697 Building REAL300004517698 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517698' /scratch/stefan/7774842/working/building/REAL300004517698 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517698 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517698/0 /scratch/stefan/7774842/working/building/REAL300004517698 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 739) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/739 `/scratch/stefan/7774842/working/3D/739' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CCC1=CC=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C1) `REAL300004517698.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517698.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517698/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517698 none O=C([O-])CCC1=CC=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [195, 193, 195, 132, 113, 106, 121, 121, 64, 35, 64, 9, 1, 1, 1, 1, 1, 1, 1, 1, 35, 40, 40, 40, 40, 121, 121, 193, 193, 132, 132, 121, 121, 9, 9, 1, 1, 1, 1, 40, 40, 40, 40, 40, 40, 40, 40, 40, 121, 121] 201 rigid atoms, others: [35, 36, 37, 38, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 788 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517698 none O=C([O-])CCC1=CC=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 5, 9, 3, 1, 1, 1, 1, 1, 1, 8, 8, 19, 48, 121, 121, 121, 121, 121, 121, 19, 26, 26, 26, 26, 1, 1, 5, 5, 3, 3, 1, 1, 48, 48, 121, 121, 121, 121, 26, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1] 201 rigid atoms, others: [32, 4, 5, 6, 7, 8, 9, 48, 49, 25, 26, 31] set([0, 1, 2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 352 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517698 none O=C([O-])CCC1=CC=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [72, 55, 72, 33, 20, 19, 26, 26, 11, 5, 11, 1, 5, 16, 40, 40, 40, 40, 40, 40, 1, 1, 1, 1, 1, 26, 26, 55, 55, 33, 33, 26, 26, 16, 16, 40, 40, 40, 40, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26] 201 rigid atoms, others: [43, 39, 40, 41, 42, 11, 44, 45, 46, 47, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 369 number of broken/clashed sets: 10 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517698 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517698 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517698/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517698 Building REAL300004517699 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517699' /scratch/stefan/7774842/working/building/REAL300004517699 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517699 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517699/0 /scratch/stefan/7774842/working/building/REAL300004517699 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 740) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/740 `/scratch/stefan/7774842/working/3D/740' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])CC1(CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)CC1) `REAL300004517699.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517699.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517699/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517699 none O=C([O-])CC1(CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [35, 35, 35, 33, 31, 24, 17, 24, 9, 1, 1, 1, 1, 1, 1, 1, 1, 17, 24, 24, 24, 24, 33, 33, 35, 35, 31, 31, 9, 9, 1, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24, 33, 33, 33, 33] 37 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 15, 16, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 166 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517699 none O=C([O-])CC1(CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [6, 4, 6, 1, 1, 1, 5, 7, 7, 12, 20, 33, 33, 33, 33, 33, 33, 12, 17, 17, 17, 17, 1, 1, 4, 4, 5, 5, 20, 20, 33, 33, 33, 33, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1] 37 rigid atoms, others: [3, 4, 5, 43, 44, 45, 46, 22, 23] set([0, 1, 2, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 138 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517699 none O=C([O-])CC1(CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)CC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [20, 18, 20, 17, 15, 12, 7, 12, 1, 7, 10, 24, 24, 24, 24, 24, 24, 1, 1, 1, 1, 1, 17, 17, 18, 18, 15, 15, 10, 10, 24, 24, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17] 37 rigid atoms, others: [34, 35, 36, 37, 38, 39, 8, 41, 42, 17, 18, 19, 20, 21, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46]) total number of confs: 103 number of broken/clashed sets: 6 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517699 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517699 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517699/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517699 Building REAL300004517700 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517700' /scratch/stefan/7774842/working/building/REAL300004517700 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517700 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517700/0 /scratch/stefan/7774842/working/building/REAL300004517700 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 741) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/741 `/scratch/stefan/7774842/working/3D/741' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1C(F)(F)C12CC(C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1)C2) `REAL300004517700.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517700.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517700/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517700 none O=C([O-])C1C(F)(F)C12CC(C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1)C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 15, 15, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [187, 186, 187, 186, 186, 186, 186, 186, 186, 87, 38, 87, 9, 1, 1, 1, 1, 1, 1, 1, 1, 38, 57, 57, 57, 57, 186, 186, 186, 186, 186, 9, 9, 1, 1, 1, 1, 57, 57, 57, 57, 57, 57, 57, 57, 57, 186, 186] 201 rigid atoms, others: [33, 34, 35, 36, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 626 number of broken/clashed sets: 49 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517700 none O=C([O-])C1C(F)(F)C12CC(C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1)C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 15, 15, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 26, 80, 186, 186, 186, 186, 186, 186, 26, 44, 44, 44, 44, 1, 1, 1, 1, 1, 80, 80, 186, 186, 186, 186, 44, 44, 44, 44, 44, 44, 44, 44, 44, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 46, 47, 26, 27, 28, 29, 30] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 524 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517700 none O=C([O-])C1C(F)(F)C12CC(C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1)C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'C.3', 'F', 'F', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 5, 15, 15, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 44, 59, 44, 44, 44, 44, 44, 44, 17, 7, 17, 1, 7, 22, 57, 57, 57, 57, 57, 57, 1, 1, 1, 1, 1, 44, 44, 44, 44, 44, 22, 22, 57, 57, 57, 57, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44] 201 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 44, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 284 number of broken/clashed sets: 49 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517700 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517700 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517700/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517700 Building REAL300004517701 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517701' /scratch/stefan/7774842/working/building/REAL300004517701 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517701 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517701/0 /scratch/stefan/7774842/working/building/REAL300004517701 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 742) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/742 `/scratch/stefan/7774842/working/3D/742' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=NC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=CS1) `REAL300004517701.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517701/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517701 none O=C([O-])C1=NC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [129, 129, 129, 129, 129, 94, 42, 94, 9, 1, 1, 1, 1, 1, 1, 1, 1, 42, 67, 67, 67, 67, 129, 129, 9, 9, 1, 1, 1, 1, 67, 67, 67, 67, 67, 67, 67, 67, 67, 129] 139 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 428 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517701 none O=C([O-])C1=NC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 8, 8, 25, 65, 129, 129, 129, 129, 129, 129, 25, 40, 40, 40, 40, 1, 1, 65, 65, 129, 129, 129, 129, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1] 139 rigid atoms, others: [1, 3, 4, 5, 6, 39, 22, 23] set([0, 2, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 383 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517701 none O=C([O-])C1=NC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=CS1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [40, 40, 40, 40, 40, 21, 10, 21, 1, 10, 29, 67, 67, 67, 67, 67, 67, 1, 1, 1, 1, 1, 40, 40, 29, 29, 67, 67, 67, 67, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40] 139 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 8, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 39]) total number of confs: 211 number of broken/clashed sets: 18 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517701 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517701 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517701/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517701 Building REAL300004517702 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517702' /scratch/stefan/7774842/working/building/REAL300004517702 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517702 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517702/0 /scratch/stefan/7774842/working/building/REAL300004517702 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 743) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/743 `/scratch/stefan/7774842/working/3D/743' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C(=O)[O-])C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1) `REAL300004517702.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517702/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517702 none COC(C(=O)[O-])C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 11, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 2, 2, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [44, 32, 12, 32, 40, 40, 5, 12, 1, 5, 17, 48, 48, 48, 48, 48, 48, 1, 1, 1, 1, 1, 44, 44, 44, 32, 17, 17, 48, 48, 48, 48, 1, 1, 1, 1, 1, 1, 1, 1, 1] 141 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 8, 17, 18, 19, 20, 21, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 15, 16, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 257 number of broken/clashed sets: 41 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517702 none COC(C(=O)[O-])C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 11, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 2, 2, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 141 conformations in input total number of sets (complete confs): 141 using faster count positions algorithm for large data unique positions, atoms: [133, 120, 64, 120, 131, 131, 34, 64, 9, 1, 1, 1, 1, 1, 1, 1, 1, 34, 48, 48, 48, 48, 133, 133, 133, 120, 9, 9, 1, 1, 1, 1, 48, 48, 48, 48, 48, 48, 48, 48, 48] 141 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 28, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 573 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517702 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517702 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517702/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517702 Building REAL300004517703 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517703' /scratch/stefan/7774842/working/building/REAL300004517703 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517703 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517703/0 /scratch/stefan/7774842/working/building/REAL300004517703 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 744) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/744 `/scratch/stefan/7774842/working/3D/744' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@]1(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C[C@H]1C(=O)[O-]) `REAL300004517703.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517703.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517703/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517703 none C[C@]1(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C[C@H]1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 5, 5, 7, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [20, 18, 16, 18, 9, 1, 1, 1, 1, 1, 1, 1, 1, 16, 18, 18, 18, 18, 20, 20, 20, 20, 20, 20, 20, 20, 20, 9, 9, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 20, 20] 22 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 12, 29, 30, 31] set([0, 1, 2, 3, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 78 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517703 none C[C@]1(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C[C@H]1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 5, 5, 7, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 3, 3, 6, 11, 20, 20, 20, 20, 20, 20, 6, 7, 7, 7, 7, 1, 1, 1, 1, 3, 3, 2, 2, 2, 11, 11, 20, 20, 20, 20, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1] 22 rigid atoms, others: [0, 1, 2, 42, 43, 18, 19, 20, 21] set([3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 73 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517703 none C[C@]1(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C[C@H]1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 5, 5, 7, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 22 conformations in input total number of sets (complete confs): 22 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 4, 6, 1, 4, 9, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 9, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 22 rigid atoms, others: [33, 34, 35, 4, 37, 38, 39, 40, 41, 13, 14, 15, 16, 17, 36] set([0, 1, 2, 3, 5, 6, 7, 8, 9, 10, 11, 12, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43]) total number of confs: 58 number of broken/clashed sets: 10 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517703 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517703 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517703/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517703 Building REAL300004517704 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517704' /scratch/stefan/7774842/working/building/REAL300004517704 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517704 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517704/0 /scratch/stefan/7774842/working/building/REAL300004517704 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 745) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/745 `/scratch/stefan/7774842/working/3D/745' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C(C(=O)[O-])S1) `REAL300004517704.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517704 none CC1=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [137, 137, 96, 39, 96, 9, 1, 1, 1, 1, 1, 1, 1, 1, 39, 67, 67, 67, 67, 137, 137, 137, 137, 137, 137, 137, 137, 137, 9, 9, 1, 1, 1, 1, 67, 67, 67, 67, 67, 67, 67, 67, 67, 137] 151 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 12, 13, 30, 31] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 466 number of broken/clashed sets: 31 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517704 none CC1=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 8, 8, 22, 66, 137, 137, 137, 137, 137, 137, 22, 41, 41, 41, 41, 1, 1, 1, 2, 2, 1, 2, 2, 2, 66, 66, 137, 137, 137, 137, 41, 41, 41, 41, 41, 41, 41, 41, 41, 1] 151 rigid atoms, others: [0, 1, 2, 3, 43, 19, 20, 21, 24] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 420 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517704 none CC1=C(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 151 conformations in input total number of sets (complete confs): 151 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 22, 10, 22, 1, 10, 29, 67, 67, 67, 67, 67, 67, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 41, 41, 41, 41, 29, 29, 67, 67, 67, 67, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41] 151 rigid atoms, others: [34, 35, 36, 5, 38, 39, 40, 41, 42, 14, 15, 16, 17, 18, 37] set([0, 1, 2, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43]) total number of confs: 212 number of broken/clashed sets: 31 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517704 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517704 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517704/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517704 Building REAL300004517705 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517705' /scratch/stefan/7774842/working/building/REAL300004517705 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517705 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517705/0 /scratch/stefan/7774842/working/building/REAL300004517705 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 746) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/746 `/scratch/stefan/7774842/working/3D/746' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=C2C=C(C(=O)N(CC3=CC=CC(F)=C3)C3CCCC3)SC2=CC=C1) `REAL300004517705.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517705/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517705 none O=C([O-])C1=C2C=C(C(=O)N(CC3=CC=CC(F)=C3)C3CCCC3)SC2=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 14, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [167, 164, 167, 164, 164, 164, 72, 34, 72, 8, 1, 1, 1, 1, 1, 1, 1, 1, 34, 60, 60, 60, 60, 164, 164, 164, 164, 164, 164, 8, 8, 1, 1, 1, 1, 60, 60, 60, 60, 60, 60, 60, 60, 60, 164, 164, 164] 201 rigid atoms, others: [32, 33, 34, 10, 11, 12, 13, 14, 15, 16, 17, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 443 number of broken/clashed sets: 35 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517705 none O=C([O-])C1=C2C=C(C(=O)N(CC3=CC=CC(F)=C3)C3CCCC3)SC2=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 14, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 10, 10, 28, 72, 164, 164, 164, 164, 164, 164, 28, 57, 57, 57, 57, 1, 1, 1, 1, 1, 1, 72, 72, 164, 164, 164, 164, 57, 57, 57, 57, 57, 57, 57, 57, 57, 1, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 44, 45, 46, 23, 24, 25, 26, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 511 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517705 none O=C([O-])C1=C2C=C(C(=O)N(CC3=CC=CC(F)=C3)C3CCCC3)SC2=CC=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 14, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [72, 57, 72, 57, 57, 57, 24, 9, 24, 1, 9, 24, 60, 60, 60, 60, 60, 60, 1, 1, 1, 1, 1, 57, 57, 57, 57, 57, 57, 24, 24, 60, 60, 60, 60, 1, 1, 1, 1, 1, 1, 1, 1, 1, 57, 57, 57] 201 rigid atoms, others: [35, 36, 37, 38, 39, 40, 9, 42, 43, 18, 19, 20, 21, 22, 41] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46]) total number of confs: 287 number of broken/clashed sets: 35 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517705 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517705 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517705/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517705 Building REAL300004517706 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517706' /scratch/stefan/7774842/working/building/REAL300004517706 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517706 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517706/0 /scratch/stefan/7774842/working/building/REAL300004517706 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 747) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/747 `/scratch/stefan/7774842/working/3D/747' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=NC=CC=C1CCC(=O)N(CC1=CC=CC(F)=C1)C1CCCC1) `REAL300004517706.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517706/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517706 none O=C([O-])C1=NC=CC=C1CCC(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 76, 76, 76, 76, 76, 76, 73, 65, 35, 25, 35, 8, 1, 1, 1, 1, 1, 1, 1, 1, 25, 32, 32, 32, 32, 76, 76, 76, 73, 73, 65, 65, 8, 8, 1, 1, 1, 1, 32, 32, 32, 32, 32, 32, 32, 32, 32] 78 rigid atoms, others: [36, 37, 38, 39, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 347 number of broken/clashed sets: 44 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517706 none O=C([O-])C1=NC=CC=C1CCC(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 4, 6, 13, 13, 33, 47, 76, 76, 76, 76, 76, 76, 33, 41, 41, 41, 41, 1, 1, 1, 4, 4, 6, 6, 47, 47, 76, 76, 76, 76, 41, 41, 41, 41, 41, 41, 41, 41, 41] 78 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 27, 28, 29] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 260 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517706 none O=C([O-])C1=NC=CC=C1CCC(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 8, 1, 1, 1, 1, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [41, 41, 41, 41, 41, 41, 41, 41, 38, 34, 11, 6, 11, 1, 6, 16, 32, 32, 32, 32, 32, 32, 1, 1, 1, 1, 1, 41, 41, 41, 38, 38, 34, 34, 16, 16, 32, 32, 32, 32, 1, 1, 1, 1, 1, 1, 1, 1, 1] 78 rigid atoms, others: [40, 41, 42, 43, 44, 13, 46, 45, 48, 22, 23, 24, 25, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 212 number of broken/clashed sets: 44 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517706 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517706 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517706/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517706 Building REAL300004517707 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517707' /scratch/stefan/7774842/working/building/REAL300004517707 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517707 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517707/0 /scratch/stefan/7774842/working/building/REAL300004517707 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 748) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/748 `/scratch/stefan/7774842/working/3D/748' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(/C=C/C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C1) `REAL300004517707.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517707.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517707/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517707 none O=C([O-])C1=CC=C(/C=C/C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [198, 198, 198, 198, 198, 198, 198, 198, 76, 38, 76, 8, 1, 1, 1, 1, 1, 1, 1, 1, 38, 44, 44, 44, 44, 198, 198, 198, 198, 198, 198, 8, 8, 1, 1, 1, 1, 44, 44, 44, 44, 44, 44, 44, 44, 44, 198, 198] 201 rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 613 number of broken/clashed sets: 32 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517707 none O=C([O-])C1=CC=C(/C=C/C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 200 conformations in input total number of sets (complete confs): 200 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 3, 3, 18, 18, 44, 110, 192, 192, 192, 192, 192, 192, 44, 67, 67, 67, 67, 1, 1, 1, 1, 3, 3, 110, 110, 192, 192, 192, 192, 67, 67, 67, 67, 67, 67, 67, 67, 67, 1, 1] 200 rigid atoms, others: [1, 3, 4, 5, 6, 7, 46, 47, 25, 26, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 645 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517707 none O=C([O-])C1=CC=C(/C=C/C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 46, 59, 46, 59, 59, 46, 46, 13, 5, 13, 1, 5, 18, 44, 44, 44, 44, 44, 44, 1, 1, 1, 1, 1, 59, 59, 59, 59, 46, 46, 18, 18, 44, 44, 44, 44, 1, 1, 1, 1, 1, 1, 1, 1, 1, 59, 59] 201 rigid atoms, others: [43, 37, 38, 39, 40, 41, 42, 11, 44, 45, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 324 number of broken/clashed sets: 32 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517707 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517707 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517707/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517707 Building REAL300004517708 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517708' /scratch/stefan/7774842/working/building/REAL300004517708 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517708 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517708/0 /scratch/stefan/7774842/working/building/REAL300004517708 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 749) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/749 `/scratch/stefan/7774842/working/3D/749' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CSC2=C1NC(C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1)=C2) `REAL300004517708.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517708.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517708/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517708 none O=C([O-])C1=CSC2=C1NC(C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1)=C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [167, 167, 167, 167, 167, 167, 167, 167, 167, 83, 35, 83, 9, 1, 1, 1, 1, 1, 1, 1, 1, 35, 65, 65, 65, 65, 167, 167, 167, 9, 9, 1, 1, 1, 1, 65, 65, 65, 65, 65, 65, 65, 65, 65, 167] 201 rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 477 number of broken/clashed sets: 36 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517708 none O=C([O-])C1=CSC2=C1NC(C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1)=C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 31, 86, 167, 167, 167, 167, 167, 167, 31, 69, 69, 69, 69, 1, 1, 1, 86, 86, 167, 167, 167, 167, 69, 69, 69, 69, 69, 69, 69, 69, 69, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 44, 26, 27, 28] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 590 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517708 none O=C([O-])C1=CSC2=C1NC(C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1)=C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [69, 69, 69, 69, 69, 69, 69, 69, 69, 29, 10, 29, 1, 10, 26, 65, 65, 65, 65, 65, 65, 1, 1, 1, 1, 1, 69, 69, 69, 26, 26, 65, 65, 65, 65, 1, 1, 1, 1, 1, 1, 1, 1, 1, 69] 201 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44]) total number of confs: 253 number of broken/clashed sets: 36 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517708 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517708 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517708/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517708 Building REAL300004517709 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517709' /scratch/stefan/7774842/working/building/REAL300004517709 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517709 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517709/0 /scratch/stefan/7774842/working/building/REAL300004517709 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 750) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/750 `/scratch/stefan/7774842/working/3D/750' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC2=C(C=C(C(=O)N(CC3=CC=CC(F)=C3)C3CCCC3)N2)S1) `REAL300004517709.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517709.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517709/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517709 none O=C([O-])C1=CC2=C(C=C(C(=O)N(CC3=CC=CC(F)=C3)C3CCCC3)N2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [184, 184, 184, 184, 184, 184, 184, 184, 86, 40, 86, 9, 1, 1, 1, 1, 1, 1, 1, 1, 40, 59, 59, 59, 59, 184, 184, 184, 184, 9, 9, 1, 1, 1, 1, 59, 59, 59, 59, 59, 59, 59, 59, 59, 184] 201 rigid atoms, others: [32, 33, 34, 12, 13, 14, 15, 16, 17, 18, 19, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 488 number of broken/clashed sets: 22 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517709 none O=C([O-])C1=CC2=C(C=C(C(=O)N(CC3=CC=CC(F)=C3)C3CCCC3)N2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 11, 11, 33, 92, 184, 184, 184, 184, 184, 184, 33, 56, 56, 56, 56, 1, 1, 1, 1, 92, 92, 184, 184, 184, 184, 56, 56, 56, 56, 56, 56, 56, 56, 56, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 44, 25, 26, 27, 28] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 587 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517709 none O=C([O-])C1=CC2=C(C=C(C(=O)N(CC3=CC=CC(F)=C3)C3CCCC3)N2)S1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 8, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 56, 56, 56, 56, 56, 56, 18, 8, 18, 1, 8, 25, 59, 59, 59, 59, 59, 59, 1, 1, 1, 1, 1, 56, 56, 56, 56, 25, 25, 59, 59, 59, 59, 1, 1, 1, 1, 1, 1, 1, 1, 1, 56] 201 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 43, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44]) total number of confs: 219 number of broken/clashed sets: 22 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517709 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517709 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517709/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517709 Building REAL300004517710 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517710' /scratch/stefan/7774842/working/building/REAL300004517710 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517710 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517710/0 /scratch/stefan/7774842/working/building/REAL300004517710 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 751) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/751 `/scratch/stefan/7774842/working/3D/751' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=COC2=C1NC(C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1)=C2) `REAL300004517710.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517710 none O=C([O-])C1=COC2=C1NC(C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1)=C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 12, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [188, 188, 188, 188, 188, 188, 188, 188, 188, 89, 42, 89, 9, 1, 1, 1, 1, 1, 1, 1, 1, 42, 65, 65, 65, 65, 188, 188, 188, 9, 9, 1, 1, 1, 1, 65, 65, 65, 65, 65, 65, 65, 65, 65, 188] 201 rigid atoms, others: [32, 33, 34, 13, 14, 15, 16, 17, 18, 19, 20, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 504 number of broken/clashed sets: 25 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517710 none O=C([O-])C1=COC2=C1NC(C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1)=C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 12, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 33, 100, 188, 188, 188, 188, 188, 188, 33, 55, 55, 55, 55, 1, 1, 1, 100, 100, 188, 188, 188, 188, 55, 55, 55, 55, 55, 55, 55, 55, 55, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 10, 44, 26, 27, 28] set([0, 2, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 599 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517710 none O=C([O-])C1=COC2=C1NC(C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1)=C2 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 12, 1, 1, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 3, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [56, 55, 56, 55, 55, 55, 55, 55, 55, 20, 8, 20, 1, 8, 25, 65, 65, 65, 65, 65, 65, 1, 1, 1, 1, 1, 55, 55, 55, 25, 25, 65, 65, 65, 65, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55] 201 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44]) total number of confs: 226 number of broken/clashed sets: 25 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517710 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517710 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517710/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517710 Building REAL300004517711 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517711' /scratch/stefan/7774842/working/building/REAL300004517711 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517711 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517711/0 /scratch/stefan/7774842/working/building/REAL300004517711 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 752) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/752 `/scratch/stefan/7774842/working/3D/752' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])C=CC=C1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1) `REAL300004517711.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517711/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517711 none CC1=C(C(=O)[O-])C=CC=C1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [128, 128, 128, 128, 128, 128, 128, 128, 128, 87, 37, 87, 8, 1, 1, 1, 1, 1, 1, 1, 1, 37, 70, 70, 70, 70, 128, 128, 128, 128, 128, 128, 8, 8, 1, 1, 1, 1, 70, 70, 70, 70, 70, 70, 70, 70, 70] 162 rigid atoms, others: [34, 35, 36, 37, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 436 number of broken/clashed sets: 43 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517711 none CC1=C(C(=O)[O-])C=CC=C1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 7, 7, 22, 60, 128, 128, 128, 128, 128, 128, 22, 51, 51, 51, 51, 2, 2, 2, 1, 1, 1, 60, 60, 128, 128, 128, 128, 51, 51, 51, 51, 51, 51, 51, 51, 51] 162 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 9, 10, 29, 30, 31] set([4, 5, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 427 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517711 none CC1=C(C(=O)[O-])C=CC=C1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 162 conformations in input total number of sets (complete confs): 162 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 51, 51, 51, 51, 51, 51, 28, 9, 28, 1, 9, 26, 70, 70, 70, 70, 70, 70, 1, 1, 1, 1, 1, 51, 51, 51, 51, 51, 51, 26, 26, 70, 70, 70, 70, 1, 1, 1, 1, 1, 1, 1, 1, 1] 162 rigid atoms, others: [38, 39, 40, 41, 42, 43, 12, 45, 46, 44, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 247 number of broken/clashed sets: 43 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517711 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517711 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517711/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517711 Building REAL300004517712 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517712' /scratch/stefan/7774842/working/building/REAL300004517712 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517712 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517712/0 /scratch/stefan/7774842/working/building/REAL300004517712 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 753) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/753 `/scratch/stefan/7774842/working/3D/753' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(C=CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=N1) `REAL300004517712.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517712 none O=C([O-])C1=CC=C(C=CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [199, 199, 199, 199, 199, 199, 120, 120, 57, 33, 57, 9, 1, 1, 1, 1, 1, 1, 1, 1, 33, 37, 37, 37, 37, 199, 199, 199, 199, 120, 120, 9, 9, 1, 1, 1, 1, 37, 37, 37, 37, 37, 37, 37, 37, 37, 199] 201 rigid atoms, others: [33, 34, 35, 36, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 540 number of broken/clashed sets: 34 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517712 none O=C([O-])C1=CC=C(C=CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 5, 5, 29, 29, 54, 117, 199, 199, 199, 199, 199, 199, 54, 59, 59, 59, 59, 1, 1, 1, 1, 5, 5, 117, 117, 199, 199, 199, 199, 59, 59, 59, 59, 59, 59, 59, 59, 59, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 46, 25, 26, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 626 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517712 none O=C([O-])C1=CC=C(C=CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=N1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 59, 59, 59, 59, 59, 25, 25, 11, 5, 11, 1, 5, 15, 37, 37, 37, 37, 37, 37, 1, 1, 1, 1, 1, 59, 59, 59, 59, 25, 25, 15, 15, 37, 37, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 59] 201 rigid atoms, others: [43, 37, 38, 39, 40, 41, 42, 11, 44, 45, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46]) total number of confs: 191 number of broken/clashed sets: 34 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517712 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517712 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517712/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517712 Building REAL300004517713 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517713' /scratch/stefan/7774842/working/building/REAL300004517713 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517713 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517713/0 /scratch/stefan/7774842/working/building/REAL300004517713 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 754) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/754 `/scratch/stefan/7774842/working/3D/754' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CSC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=C1) `REAL300004517713.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517713 none O=C([O-])C1=CSC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [165, 165, 165, 165, 165, 165, 84, 35, 84, 8, 1, 1, 1, 1, 1, 1, 1, 1, 35, 66, 66, 66, 66, 165, 165, 8, 8, 1, 1, 1, 1, 66, 66, 66, 66, 66, 66, 66, 66, 66, 165] 201 rigid atoms, others: [10, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 491 number of broken/clashed sets: 45 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517713 none O=C([O-])C1=CSC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 32, 74, 165, 165, 165, 165, 165, 165, 32, 66, 66, 66, 66, 1, 1, 74, 74, 165, 165, 165, 165, 66, 66, 66, 66, 66, 66, 66, 66, 66, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 40, 23, 24] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 510 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517713 none O=C([O-])C1=CSC(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [66, 66, 66, 66, 66, 66, 26, 9, 26, 1, 9, 25, 66, 66, 66, 66, 66, 66, 1, 1, 1, 1, 1, 66, 66, 25, 25, 66, 66, 66, 66, 1, 1, 1, 1, 1, 1, 1, 1, 1, 66] 201 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 9, 18, 19, 20, 21, 22, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 25, 26, 27, 28, 29, 30, 40]) total number of confs: 256 number of broken/clashed sets: 45 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517713 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517713 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517713/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517713 Building REAL300004517714 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517714' /scratch/stefan/7774842/working/building/REAL300004517714 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517714 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517714/0 /scratch/stefan/7774842/working/building/REAL300004517714 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 755) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/755 `/scratch/stefan/7774842/working/3D/755' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])[C@H]1[C@@H]2CC[C@@H](O2)[C@H]1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1) `REAL300004517714.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517714 none O=C([O-])[C@H]1[C@@H]2CC[C@@H](O2)[C@H]1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 7, 5, 5, 5, 7, 12, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 40, 27, 40, 9, 1, 1, 1, 1, 1, 1, 1, 1, 27, 30, 30, 30, 30, 40, 40, 40, 40, 9, 9, 1, 1, 1, 1, 30, 30, 30, 30, 30, 30, 30, 30, 30] 41 rigid atoms, others: [36, 37, 38, 39, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 138 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517714 none O=C([O-])[C@H]1[C@@H]2CC[C@@H](O2)[C@H]1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 7, 5, 5, 5, 7, 12, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 21, 40, 40, 40, 40, 40, 40, 9, 11, 11, 11, 11, 1, 1, 1, 1, 21, 21, 40, 40, 40, 40, 11, 11, 11, 11, 11, 11, 11, 11, 11] 41 rigid atoms, others: [32, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 33, 30, 31] set([0, 2, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 121 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517714 none O=C([O-])[C@H]1[C@@H]2CC[C@@H](O2)[C@H]1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 5, 7, 5, 7, 5, 5, 5, 7, 12, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 10, 11, 6, 10, 1, 6, 15, 30, 30, 30, 30, 30, 30, 1, 1, 1, 1, 1, 11, 11, 11, 11, 15, 15, 30, 30, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1] 41 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 25, 26, 27, 28, 29] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 90 number of broken/clashed sets: 9 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517714 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517714 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517714/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517714 Building REAL300004517715 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517715' /scratch/stefan/7774842/working/building/REAL300004517715 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517715 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517715/0 /scratch/stefan/7774842/working/building/REAL300004517715 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 756) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/756 `/scratch/stefan/7774842/working/3D/756' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=CC2=C(C(=O)N(CC3=CC=CC(F)=C3)C3CCCC3)C=CC=C12) `REAL300004517715.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517715.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517715/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517715 none O=C([O-])C1=CC=CC2=C(C(=O)N(CC3=CC=CC(F)=C3)C3CCCC3)C=CC=C12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [173, 173, 173, 173, 173, 173, 173, 173, 90, 36, 90, 8, 1, 1, 1, 1, 1, 1, 1, 1, 36, 65, 65, 65, 65, 173, 173, 173, 173, 173, 173, 173, 8, 8, 1, 1, 1, 1, 65, 65, 65, 65, 65, 65, 65, 65, 65, 173, 173, 173] 201 rigid atoms, others: [34, 35, 36, 37, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 498 number of broken/clashed sets: 54 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517715 none O=C([O-])C1=CC=CC2=C(C(=O)N(CC3=CC=CC(F)=C3)C3CCCC3)C=CC=C12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 7, 7, 25, 77, 173, 173, 173, 173, 173, 173, 25, 55, 55, 55, 55, 1, 1, 1, 1, 1, 1, 1, 77, 77, 173, 173, 173, 173, 55, 55, 55, 55, 55, 55, 55, 55, 55, 1, 1, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 8, 9, 47, 48, 49, 25, 26, 27, 28, 29, 30, 31] set([0, 2, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 535 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517715 none O=C([O-])C1=CC=CC2=C(C(=O)N(CC3=CC=CC(F)=C3)C3CCCC3)C=CC=C12 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [64, 55, 64, 55, 55, 55, 55, 55, 27, 9, 27, 1, 9, 25, 65, 65, 65, 65, 65, 65, 1, 1, 1, 1, 1, 55, 55, 55, 55, 55, 55, 55, 25, 25, 65, 65, 65, 65, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55] 201 rigid atoms, others: [43, 38, 39, 40, 41, 42, 11, 44, 45, 46, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, 18, 19, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 280 number of broken/clashed sets: 54 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517715 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517715 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517715/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517715 Building REAL300004517716 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517716' /scratch/stefan/7774842/working/building/REAL300004517716 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517716 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517716/0 /scratch/stefan/7774842/working/building/REAL300004517716 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 757) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/757 `/scratch/stefan/7774842/working/3D/757' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@]1(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C[C@H]1C(=O)[O-]) `REAL300004517716.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517716.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517716/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517716 none CC(C)[C@]1(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C[C@H]1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 5, 5, 7, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 9, 7, 1, 1, 1, 1, 1, 1, 1, 1, 9, 11, 11, 11, 11, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 7, 7, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 9, 9] 11 rigid atoms, others: [35, 36, 37, 38, 7, 8, 9, 10, 11, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 38 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517716 none CC(C)[C@]1(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C[C@H]1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 5, 5, 7, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 1, 1, 3, 3, 3, 4, 9, 9, 9, 9, 9, 9, 3, 4, 4, 4, 4, 1, 1, 1, 1, 2, 2, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1] 11 rigid atoms, others: [1, 3, 4, 48, 49, 20, 21, 22, 23] set([0, 2, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 41 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517716 none CC(C)[C@]1(C(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C[C@H]1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 5, 5, 7, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [5, 4, 5, 4, 3, 4, 1, 3, 5, 11, 11, 11, 11, 11, 11, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 11 rigid atoms, others: [6, 39, 40, 41, 42, 43, 44, 45, 46, 15, 16, 17, 18, 19, 47] set([0, 1, 2, 3, 4, 5, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 36 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517716 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517716 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517716/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517716 Building REAL300004517717 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517717' /scratch/stefan/7774842/working/building/REAL300004517717 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517717 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517717/0 /scratch/stefan/7774842/working/building/REAL300004517717 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 758) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/758 `/scratch/stefan/7774842/working/3D/758' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC(C(=O)[O-])=CC=C1CC(=O)N(CC1=CC=CC(F)=C1)C1CCCC1) `REAL300004517717.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517717.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517717/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517717 none CC1=CC(C(=O)[O-])=CC=C1CC(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [140, 140, 140, 140, 140, 140, 140, 140, 140, 100, 41, 29, 41, 8, 1, 1, 1, 1, 1, 1, 1, 1, 29, 34, 34, 34, 34, 140, 140, 140, 140, 140, 140, 100, 100, 8, 8, 1, 1, 1, 1, 34, 34, 34, 34, 34, 34, 34, 34, 34] 140 rigid atoms, others: [37, 38, 39, 40, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 466 number of broken/clashed sets: 70 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517717 none CC1=CC(C(=O)[O-])=CC=C1CC(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 6, 19, 19, 49, 85, 140, 140, 140, 140, 140, 140, 49, 56, 56, 56, 56, 2, 2, 2, 1, 1, 1, 6, 6, 85, 85, 140, 140, 140, 140, 56, 56, 56, 56, 56, 56, 56, 56, 56] 140 rigid atoms, others: [0, 1, 2, 3, 4, 7, 8, 9, 10, 32, 30, 31] set([5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 478 number of broken/clashed sets: 70 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517717 none CC1=CC(C(=O)[O-])=CC=C1CC(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 56, 56, 56, 56, 56, 56, 56, 40, 11, 6, 11, 1, 6, 16, 34, 34, 34, 34, 34, 34, 1, 1, 1, 1, 1, 56, 56, 56, 56, 56, 56, 40, 40, 16, 16, 34, 34, 34, 34, 1, 1, 1, 1, 1, 1, 1, 1, 1] 140 rigid atoms, others: [41, 42, 43, 44, 13, 46, 45, 48, 49, 22, 23, 24, 25, 26, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 239 number of broken/clashed sets: 70 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517717 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517717 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517717/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517717 Building REAL300004517718 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517718' /scratch/stefan/7774842/working/building/REAL300004517718 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517718 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517718/0 /scratch/stefan/7774842/working/building/REAL300004517718 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 759) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/759 `/scratch/stefan/7774842/working/3D/759' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CSC(CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=C1) `REAL300004517718.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517718.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517718/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517718 none O=C([O-])C1=CSC(CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [189, 189, 189, 189, 189, 189, 109, 55, 36, 55, 9, 1, 1, 1, 1, 1, 1, 1, 1, 36, 40, 40, 40, 40, 189, 189, 109, 109, 9, 9, 1, 1, 1, 1, 40, 40, 40, 40, 40, 40, 40, 40, 40, 189] 201 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 546 number of broken/clashed sets: 71 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517718 none O=C([O-])C1=CSC(CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 8, 34, 34, 64, 112, 189, 189, 189, 189, 189, 189, 64, 74, 74, 74, 74, 1, 1, 8, 8, 112, 112, 189, 189, 189, 189, 74, 74, 74, 74, 74, 74, 74, 74, 74, 1] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 43, 24, 25] set([8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 607 number of broken/clashed sets: 71 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517718 none O=C([O-])C1=CSC(CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)=C1 NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 14, 1, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [74, 74, 74, 74, 74, 74, 33, 12, 5, 12, 1, 5, 17, 40, 40, 40, 40, 40, 40, 1, 1, 1, 1, 1, 74, 74, 33, 33, 17, 17, 40, 40, 40, 40, 1, 1, 1, 1, 1, 1, 1, 1, 1, 74] 201 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 10, 19, 20, 21, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43]) total number of confs: 259 number of broken/clashed sets: 71 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517718 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517718 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517718/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517718 Building REAL300004517719 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517719' /scratch/stefan/7774842/working/building/REAL300004517719 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517719 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517719/0 /scratch/stefan/7774842/working/building/REAL300004517719 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 760) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/760 `/scratch/stefan/7774842/working/3D/760' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C([O-])C1=CC=C(CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C1F) `REAL300004517719.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517719.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517719/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517719 none O=C([O-])C1=CC=C(CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [200, 197, 200, 197, 197, 197, 108, 48, 30, 48, 8, 1, 1, 1, 1, 1, 1, 1, 1, 30, 35, 35, 35, 35, 197, 197, 197, 197, 197, 108, 108, 8, 8, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35, 35, 35, 35, 197] 201 rigid atoms, others: [33, 34, 35, 36, 11, 12, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 614 number of broken/clashed sets: 60 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517719 none O=C([O-])C1=CC=C(CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 3, 1, 1, 1, 1, 1, 6, 23, 23, 64, 113, 197, 197, 197, 197, 197, 197, 64, 74, 74, 74, 74, 1, 1, 1, 1, 1, 6, 6, 113, 113, 197, 197, 197, 197, 74, 74, 74, 74, 74, 74, 74, 74, 74, 1] 201 rigid atoms, others: [1, 3, 4, 5, 6, 7, 46, 24, 25, 26, 27, 28] set([0, 2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 633 number of broken/clashed sets: 60 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517719 none O=C([O-])C1=CC=C(CC(=O)N(CC2=CC=CC(F)=C2)C2CCCC2)C=C1F NO_LONG_NAME dock atom types: ['O.co2', 'C.2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 11, 1, 1, 1, 1, 5, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [2, 7, 2, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [78, 74, 78, 74, 74, 74, 41, 12, 5, 12, 1, 5, 15, 35, 35, 35, 35, 35, 35, 1, 1, 1, 1, 1, 74, 74, 74, 74, 74, 41, 41, 15, 15, 35, 35, 35, 35, 1, 1, 1, 1, 1, 1, 1, 1, 1, 74] 201 rigid atoms, others: [37, 38, 39, 40, 41, 10, 43, 44, 45, 19, 20, 21, 22, 23, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46]) total number of confs: 296 number of broken/clashed sets: 60 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517719 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517719 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517719/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517719 Building REAL300004517720 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517720' /scratch/stefan/7774842/working/building/REAL300004517720 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517720 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517720/0 /scratch/stefan/7774842/working/building/REAL300004517720 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 761) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/761 `/scratch/stefan/7774842/working/3D/761' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1(C)[C@H](C(=O)[O-])[C@@H]1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1) `REAL300004517720.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517720.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517720/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517720 none CC1(C)[C@H](C(=O)[O-])[C@@H]1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 11, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 16, 19, 9, 1, 1, 1, 1, 1, 1, 1, 1, 16, 21, 21, 21, 21, 19, 19, 19, 19, 19, 19, 9, 9, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21] 23 rigid atoms, others: [34, 35, 36, 37, 13, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 84 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517720 none CC1(C)[C@H](C(=O)[O-])[C@@H]1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 11, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 2, 2, 4, 9, 19, 19, 19, 19, 19, 19, 4, 7, 7, 7, 7, 1, 1, 1, 2, 2, 2, 9, 9, 19, 19, 19, 19, 7, 7, 7, 7, 7, 7, 7, 7, 7] 23 rigid atoms, others: [0, 1, 2, 3, 4, 5, 8, 9, 10, 26, 27, 28] set([6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 67 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517720 none CC1(C)[C@H](C(=O)[O-])[C@@H]1C(=O)N(CC1=CC=CC(F)=C1)C1CCCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 1, 11, 11, 5, 7, 1, 11, 8, 5, 1, 1, 1, 1, 1, 15, 1, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 5, 7, 1, 5, 11, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 11, 11, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1] 23 rigid atoms, others: [38, 39, 40, 41, 42, 43, 12, 45, 46, 44, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 60 number of broken/clashed sets: 6 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517720 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517720 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517720/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517720 Building REAL300004517721 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517721' /scratch/stefan/7774842/working/building/REAL300004517721 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517721 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517721/0 /scratch/stefan/7774842/working/building/REAL300004517721 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 762) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/762 `/scratch/stefan/7774842/working/3D/762' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC=C(C(=O)[O-])C=C1) `REAL300004517721.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517721/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517721 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 35, 56, 56, 57, 26, 12, 5, 12, 20, 21, 21, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 56, 56, 56, 56, 56, 57, 57, 57, 57, 57, 35, 35, 26, 26, 20, 20, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1] 61 rigid atoms, others: [48, 50, 49, 13, 47, 16, 17, 18, 19, 20, 21, 22, 23, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 313 number of broken/clashed sets: 61 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517721 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517721 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517721/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517721 Building REAL300004517722 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517722' /scratch/stefan/7774842/working/building/REAL300004517722 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517722 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517722/0 /scratch/stefan/7774842/working/building/REAL300004517722 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 763) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/763 `/scratch/stefan/7774842/working/3D/763' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC=CC(OCC(=O)[O-])=C1) `REAL300004517722.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517722.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517722/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517722 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC=CC(OCC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [23, 21, 16, 21, 21, 22, 15, 13, 6, 13, 15, 15, 15, 1, 6, 1, 1, 1, 1, 1, 1, 4, 10, 14, 14, 1, 23, 23, 23, 23, 23, 22, 22, 22, 22, 22, 16, 16, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 10, 10, 1] 35 rigid atoms, others: [51, 50, 17, 13, 15, 16, 49, 18, 19, 20, 54, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 52, 53]) total number of confs: 156 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517722 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517722 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517722/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517722 Building REAL300004517723 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517723' /scratch/stefan/7774842/working/building/REAL300004517723 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517723 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517723/0 /scratch/stefan/7774842/working/building/REAL300004517723 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 764) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/764 `/scratch/stefan/7774842/working/3D/764' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC=CC(C(=O)[O-])=C1) `REAL300004517723.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517723/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517723 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 19, 19, 19, 19, 19, 19, 11, 8, 11, 13, 13, 13, 1, 8, 1, 1, 1, 1, 1, 1, 2, 2, 1, 20, 20, 20, 20, 20, 19, 19, 19, 19, 19, 19, 19, 19, 19, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1, 1] 20 rigid atoms, others: [48, 50, 49, 13, 47, 16, 17, 18, 19, 20, 23, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 90 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517723 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517723 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517723/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517723 Building REAL300004517724 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517724' /scratch/stefan/7774842/working/building/REAL300004517724 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517724 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517724/0 /scratch/stefan/7774842/working/building/REAL300004517724 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 765) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/765 `/scratch/stefan/7774842/working/3D/765' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC=C(C(=O)[O-])S1) `REAL300004517724.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517724/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517724 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 35 conformations in input total number of sets (complete confs): 35 using default count positions algorithm for smaller data unique positions, atoms: [29, 24, 24, 24, 24, 30, 24, 14, 9, 14, 16, 16, 16, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 30, 30, 30, 30, 30, 24, 24, 24, 24, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1] 35 rigid atoms, others: [13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 160 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517724 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517724 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517724/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517724 Building REAL300004517725 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517725' /scratch/stefan/7774842/working/building/REAL300004517725 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517725 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517725/0 /scratch/stefan/7774842/working/building/REAL300004517725 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 766) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/766 `/scratch/stefan/7774842/working/3D/766' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC=CC(C(=O)[O-])=N1) `REAL300004517725.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517725 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC=CC(C(=O)[O-])=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 12, 12, 12, 12, 12, 12, 6, 5, 6, 7, 7, 7, 1, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 13, 13, 13, 13, 13, 12, 12, 12, 12, 12, 12, 12, 12, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1] 13 rigid atoms, others: [48, 49, 13, 47, 16, 17, 18, 19, 20, 23, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 61 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517725 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517725 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517725/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517725 Building REAL300004517726 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517726' /scratch/stefan/7774842/working/building/REAL300004517726 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517726 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517726/0 /scratch/stefan/7774842/working/building/REAL300004517726 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 767) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/767 `/scratch/stefan/7774842/working/3D/767' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOC1=CC(C(=O)N(CC[NH+](CC)CC)CC(C)C)=CC=C1OCC(=O)[O-]) `REAL300004517726.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517726/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517726 none CCOC1=CC(C(=O)N(CC[NH+](CC)CC)CC(C)C)=CC=C1OCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 9, 6, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 12, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 4, 4, 4, 4, 4, 3, 6, 6, 6, 1, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 1, 3, 3, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 7, 7] 9 rigid atoms, others: [34, 3, 4, 5, 6, 2, 21, 22, 23, 24, 58, 59] set([0, 1, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 60, 61]) total number of confs: 57 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517726 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517726 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517726/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517726 Building REAL300004517727 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517727' /scratch/stefan/7774842/working/building/REAL300004517727 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517727 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517727/0 /scratch/stefan/7774842/working/building/REAL300004517727 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 768) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/768 `/scratch/stefan/7774842/working/3D/768' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)CCC1=CC=C(C(=O)[O-])C=C1) `REAL300004517727.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517727.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517727/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517727 none CC[NH+](CC)CCN(CC(C)C)C(=O)CCC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 4 conformations in input total number of sets (complete confs): 4 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1] 4 rigid atoms, others: [19, 22, 55, 15, 16, 17, 18, 51, 52, 53, 54, 23, 24, 25, 56, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 16 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517727 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517727 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517727/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517727 Building REAL300004517728 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517728' /scratch/stefan/7774842/working/building/REAL300004517728 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517728 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517728/0 /scratch/stefan/7774842/working/building/REAL300004517728 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 769) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/769 `/scratch/stefan/7774842/working/3D/769' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC=NC(C(=O)[O-])=C1) `REAL300004517728.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517728.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517728/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517728 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC=NC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 1, 8, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [19, 18, 18, 18, 18, 18, 18, 11, 8, 11, 13, 13, 13, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 18, 18, 18, 18, 18, 18, 18, 18, 18, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1] 19 rigid atoms, others: [48, 49, 13, 47, 16, 17, 18, 19, 20, 21, 22, 23, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 83 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517728 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517728 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517728/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517728 Building REAL300004517729 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517729' /scratch/stefan/7774842/working/building/REAL300004517729 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517729 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517729/0 /scratch/stefan/7774842/working/building/REAL300004517729 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 770) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/770 `/scratch/stefan/7774842/working/3D/770' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C=CC1=CC=C(C(=O)[O-])C=C1) `REAL300004517729.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517729 none CC[NH+](CC)CCN(CC(C)C)C(=O)C=CC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [140, 134, 131, 133, 134, 140, 127, 55, 19, 55, 75, 75, 75, 3, 19, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 140, 140, 140, 140, 140, 140, 140, 140, 140, 140, 131, 131, 127, 127, 75, 75, 75, 75, 75, 75, 75, 75, 75, 3, 3, 1, 1, 1, 1] 140 rigid atoms, others: [51, 54, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 697 number of broken/clashed sets: 140 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517729 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517729 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517729/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517729 Building REAL300004517730 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517730' /scratch/stefan/7774842/working/building/REAL300004517730 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517730 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517730/0 /scratch/stefan/7774842/working/building/REAL300004517730 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 771) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/771 `/scratch/stefan/7774842/working/3D/771' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC(C(=O)[O-])=CC([N+](=O)[O-])=C1) `REAL300004517730.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517730/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517730 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC(C(=O)[O-])=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 22, 22, 22, 22, 22, 22, 12, 8, 12, 15, 15, 15, 1, 8, 1, 1, 1, 1, 2, 2, 1, 1, 1, 2, 2, 1, 23, 23, 23, 23, 23, 22, 22, 22, 22, 22, 22, 22, 22, 22, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1] 23 rigid atoms, others: [18, 13, 15, 16, 17, 50, 51, 52, 21, 22, 23, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 19, 20, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 111 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517730 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517730 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517730/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517730 Building REAL300004517731 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517731' /scratch/stefan/7774842/working/building/REAL300004517731 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517731 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517731/0 /scratch/stefan/7774842/working/building/REAL300004517731 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 772) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/772 `/scratch/stefan/7774842/working/3D/772' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC(C(=O)[O-])=CC([N+](=O)[O-])=C1) `REAL300004517731.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517731/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517731 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC(C(=O)[O-])=CC([N+](=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 22, 22, 22, 22, 22, 22, 12, 8, 12, 15, 15, 15, 1, 8, 1, 1, 1, 1, 2, 2, 1, 1, 1, 2, 2, 1, 23, 23, 23, 23, 23, 22, 22, 22, 22, 22, 22, 22, 22, 22, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1] 23 rigid atoms, others: [18, 13, 15, 16, 17, 50, 51, 52, 21, 22, 23, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 19, 20, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 111 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517731 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517731 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517731/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517731 Building REAL300004517732 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517732' /scratch/stefan/7774842/working/building/REAL300004517732 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517732 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517732/0 /scratch/stefan/7774842/working/building/REAL300004517732 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 773) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/773 `/scratch/stefan/7774842/working/3D/773' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC=C(C(=O)[O-])O1) `REAL300004517732.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517732 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [22, 18, 18, 18, 18, 21, 18, 10, 6, 10, 10, 10, 10, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 21, 21, 21, 21, 21, 18, 18, 18, 18, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1] 25 rigid atoms, others: [13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 109 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517732 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517732 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517732/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517732 Building REAL300004517733 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517733' /scratch/stefan/7774842/working/building/REAL300004517733 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517733 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517733/0 /scratch/stefan/7774842/working/building/REAL300004517733 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 774) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/774 `/scratch/stefan/7774842/working/3D/774' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)CCC1=CC=CC=C1C(=O)[O-]) `REAL300004517733.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517733.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517733/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517733 none CC[NH+](CC)CCN(CC(C)C)C(=O)CCC1=CC=CC=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 10, 12, 12, 12, 10, 9, 7, 9, 9, 9, 9, 3, 7, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 10, 10, 10, 10, 9, 9, 9, 9, 9, 9, 9, 9, 9, 3, 3, 3, 3, 1, 1, 1, 1] 12 rigid atoms, others: [54, 23, 16, 17, 18, 19, 20, 53, 22, 55, 56, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 52 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517733 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517733 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517733/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517733 Building REAL300004517734 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517734' /scratch/stefan/7774842/working/building/REAL300004517734 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517734 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517734/0 /scratch/stefan/7774842/working/building/REAL300004517734 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 775) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/775 `/scratch/stefan/7774842/working/3D/775' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC(C)=C(OCC(=O)[O-])C(C)=C1) `REAL300004517734.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517734 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC(C)=C(OCC(=O)[O-])C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 1, 5, 1, 12, 5, 1, 11, 11, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [18, 17, 10, 17, 17, 17, 10, 5, 4, 5, 10, 10, 10, 1, 4, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 1, 1, 1, 18, 18, 18, 18, 18, 17, 17, 17, 17, 17, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 2, 2, 2, 4, 4, 2, 2, 2, 1] 19 rigid atoms, others: [19, 13, 15, 16, 17, 18, 51, 20, 25, 26, 27, 60] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 52, 53, 54, 55, 56, 57, 58, 59]) total number of confs: 126 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517734 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517734 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517734/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517734 Building REAL300004517735 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517735' /scratch/stefan/7774842/working/building/REAL300004517735 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517735 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517735/0 /scratch/stefan/7774842/working/building/REAL300004517735 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 776) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/776 `/scratch/stefan/7774842/working/3D/776' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)CC1=CC=CC(C(=O)[O-])=C1) `REAL300004517735.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517735.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517735/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517735 none CC[NH+](CC)CCN(CC(C)C)C(=O)CC1=CC=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 48 conformations in input total number of sets (complete confs): 48 using default count positions algorithm for smaller data unique positions, atoms: [48, 45, 28, 45, 45, 47, 27, 16, 13, 16, 18, 18, 18, 6, 13, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 48, 48, 48, 48, 48, 47, 47, 47, 47, 47, 28, 28, 27, 27, 18, 18, 18, 18, 18, 18, 18, 18, 18, 6, 6, 1, 1, 1, 1] 48 rigid atoms, others: [51, 50, 15, 16, 17, 18, 19, 20, 21, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 235 number of broken/clashed sets: 48 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517735 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517735 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517735/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517735 Building REAL300004517736 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517736' /scratch/stefan/7774842/working/building/REAL300004517736 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517736 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517736/0 /scratch/stefan/7774842/working/building/REAL300004517736 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 777) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/777 `/scratch/stefan/7774842/working/3D/777' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1CCCC(C(=O)[O-])C1) `REAL300004517736.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517736/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517736 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1CCCC(C(=O)[O-])C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 3 rigid atoms, others: [19, 48, 50, 49, 55, 13, 47, 16, 17, 18, 51, 52, 53, 54, 23, 56, 20, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 11 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517736 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517736 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517736/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517736 Building REAL300004517737 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517737' /scratch/stefan/7774842/working/building/REAL300004517737 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517737 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517737/0 /scratch/stefan/7774842/working/building/REAL300004517737 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 778) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/778 `/scratch/stefan/7774842/working/3D/778' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC=C(C(=O)[O-])N=C1) `REAL300004517737.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517737.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517737/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517737 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC=C(C(=O)[O-])N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 11, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 92 conformations in input total number of sets (complete confs): 92 using faster count positions algorithm for large data unique positions, atoms: [86, 86, 58, 86, 86, 87, 44, 20, 9, 20, 31, 32, 32, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 86, 86, 86, 86, 86, 87, 87, 87, 87, 87, 58, 58, 44, 44, 31, 31, 32, 32, 32, 32, 32, 32, 32, 1, 1, 1] 92 rigid atoms, others: [48, 49, 13, 47, 16, 17, 18, 19, 20, 21, 22, 23, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 482 number of broken/clashed sets: 92 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517737 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517737 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517737/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517737 Building REAL300004517738 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517738' /scratch/stefan/7774842/working/building/REAL300004517738 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517738 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517738/0 /scratch/stefan/7774842/working/building/REAL300004517738 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 779) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/779 `/scratch/stefan/7774842/working/3D/779' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC=C(C(=O)[O-])C=N1) `REAL300004517738.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517738.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517738/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517738 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC=C(C(=O)[O-])C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [18, 17, 13, 17, 17, 18, 10, 7, 5, 7, 9, 9, 9, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 13, 13, 10, 10, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1] 20 rigid atoms, others: [48, 49, 13, 47, 16, 17, 18, 19, 20, 21, 22, 23, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 100 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517738 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517738 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517738/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517738 Building REAL300004517739 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517739' /scratch/stefan/7774842/working/building/REAL300004517739 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517739 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517739/0 /scratch/stefan/7774842/working/building/REAL300004517739 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 780) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/780 `/scratch/stefan/7774842/working/3D/780' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)CC(C)(C)CC(=O)[O-]) `REAL300004517739.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517739.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517739/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.0.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.0.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.0.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517739 none CC[NH+](CC)CCN(CC(C)C)C(=O)CC(C)(C)CC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 6, 6, 6, 8, 5, 1, 1, 1, 3, 4, 4, 1, 3, 3, 5, 11, 11, 11, 12, 13, 13, 7, 7, 7, 7, 7, 8, 8, 8, 8, 8, 6, 6, 5, 5, 3, 3, 4, 4, 4, 4, 4, 4, 4, 5, 5, 11, 11, 11, 11, 11, 11, 12, 12] 16 rigid atoms, others: [8, 9, 13, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 107 number of broken/clashed sets: 16 ./output.0.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517739 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517739 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517739/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517739 Building REAL300004517740 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517740' /scratch/stefan/7774842/working/building/REAL300004517740 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517740 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517740/0 /scratch/stefan/7774842/working/building/REAL300004517740 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 781) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/781 `/scratch/stefan/7774842/working/3D/781' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC=C(C(=O)[O-])C=C1F) `REAL300004517740.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517740 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC=C(C(=O)[O-])C=C1F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [19, 19, 17, 19, 19, 19, 16, 11, 6, 11, 16, 16, 16, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 17, 17, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 1, 1, 1] 20 rigid atoms, others: [48, 50, 49, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 101 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517740 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517740 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517740/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517740 Building REAL300004517741 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517741' /scratch/stefan/7774842/working/building/REAL300004517741 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517741 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517741/0 /scratch/stefan/7774842/working/building/REAL300004517741 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 782) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/782 `/scratch/stefan/7774842/working/3D/782' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CN=C(C(=O)[O-])C=N1) `REAL300004517741.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517741/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517741 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CN=C(C(=O)[O-])C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 8, 1, 1, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [27, 26, 20, 26, 26, 28, 16, 11, 5, 11, 14, 14, 14, 1, 5, 1, 1, 1, 1, 1, 2, 2, 1, 1, 27, 27, 27, 27, 27, 28, 28, 28, 28, 28, 20, 20, 16, 16, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1] 30 rigid atoms, others: [48, 13, 47, 16, 17, 18, 19, 22, 23, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 155 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517741 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517741 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517741/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517741 Building REAL300004517742 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517742' /scratch/stefan/7774842/working/building/REAL300004517742 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517742 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517742/0 /scratch/stefan/7774842/working/building/REAL300004517742 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 783) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/783 `/scratch/stefan/7774842/working/3D/783' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)[C@H]1CC[C@H](C(=O)[O-])CC1) `REAL300004517742.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517742 none CC[NH+](CC)CCN(CC(C)C)C(=O)[C@H]1CC[C@H](C(=O)[O-])CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 67 conformations in input total number of sets (complete confs): 67 using faster count positions algorithm for large data unique positions, atoms: [59, 57, 32, 57, 57, 59, 24, 16, 6, 16, 21, 23, 23, 1, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 59, 59, 59, 59, 59, 59, 59, 59, 59, 59, 32, 32, 24, 24, 21, 21, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1] 67 rigid atoms, others: [51, 50, 56, 49, 13, 15, 16, 17, 18, 19, 52, 21, 54, 55, 24, 25, 20, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 322 number of broken/clashed sets: 67 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517742 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517742 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517742/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517742 Building REAL300004517743 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517743' /scratch/stefan/7774842/working/building/REAL300004517743 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517743 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517743/0 /scratch/stefan/7774842/working/building/REAL300004517743 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 784) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/784 `/scratch/stefan/7774842/working/3D/784' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1CCC(C(=O)[O-])CC1) `REAL300004517743.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517743.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517743/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517743 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1CCC(C(=O)[O-])CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 5, 5, 5, 5, 1, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [61, 57, 32, 57, 57, 62, 24, 16, 6, 16, 21, 23, 23, 1, 6, 1, 1, 1, 1, 1, 3, 3, 1, 1, 61, 61, 61, 61, 61, 62, 62, 62, 62, 62, 32, 32, 24, 24, 21, 21, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 71 rigid atoms, others: [19, 48, 50, 54, 49, 55, 13, 47, 16, 17, 18, 51, 52, 53, 22, 23, 56, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 352 number of broken/clashed sets: 71 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517743 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517743 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517743/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517743 Building REAL300004517744 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517744' /scratch/stefan/7774842/working/building/REAL300004517744 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517744 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517744/0 /scratch/stefan/7774842/working/building/REAL300004517744 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 785) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/785 `/scratch/stefan/7774842/working/3D/785' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)CC1=CC=C(C(=O)[O-])C=C1) `REAL300004517744.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517744.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517744/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517744 none CC[NH+](CC)CCN(CC(C)C)C(=O)CC1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 54 conformations in input total number of sets (complete confs): 54 using faster count positions algorithm for large data unique positions, atoms: [54, 54, 36, 54, 54, 54, 31, 21, 12, 21, 24, 24, 24, 3, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 54, 54, 54, 54, 54, 54, 54, 54, 54, 54, 36, 36, 31, 31, 24, 24, 24, 24, 24, 24, 24, 24, 24, 3, 3, 1, 1, 1, 1] 54 rigid atoms, others: [51, 50, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 273 number of broken/clashed sets: 54 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517744 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517744 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517744/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517744 Building REAL300004517745 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517745' /scratch/stefan/7774842/working/building/REAL300004517745 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517745 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517745/0 /scratch/stefan/7774842/working/building/REAL300004517745 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 786) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/786 `/scratch/stefan/7774842/working/3D/786' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)CN1C=C(C(=O)[O-])N=N1) `REAL300004517745.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517745.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517745/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517745 none CC[NH+](CC)CCN(CC(C)C)C(=O)CN1C=C(C(=O)[O-])N=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 5, 8, 1, 1, 1, 11, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 8, 10, 10, 10, 8, 8, 7, 8, 8, 8, 8, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 5, 5, 1] 10 rigid atoms, others: [49, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 40 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517745 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517745 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517745/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517745 Building REAL300004517746 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517746' /scratch/stefan/7774842/working/building/REAL300004517746 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517746 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517746/0 /scratch/stefan/7774842/working/building/REAL300004517746 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 787) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/787 `/scratch/stefan/7774842/working/3D/787' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC=C(C(=O)[O-])C(C)=N1) `REAL300004517746.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517746/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517746 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC=C(C(=O)[O-])C(C)=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 26 conformations in input total number of sets (complete confs): 26 using default count positions algorithm for smaller data unique positions, atoms: [24, 23, 15, 23, 23, 24, 12, 7, 5, 7, 10, 10, 10, 1, 5, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 24, 24, 24, 24, 24, 24, 24, 24, 24, 24, 15, 15, 12, 12, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 1, 2, 2, 2] 26 rigid atoms, others: [48, 49, 13, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 50, 51, 52]) total number of confs: 148 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517746 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517746 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517746/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517746 Building REAL300004517747 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517747' /scratch/stefan/7774842/working/building/REAL300004517747 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517747 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517747/0 /scratch/stefan/7774842/working/building/REAL300004517747 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 788) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/788 `/scratch/stefan/7774842/working/3D/788' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC(Br)=CC(C(=O)[O-])=C1) `REAL300004517747.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517747.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517747/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517747 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC(Br)=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 1, 17, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 20, 20, 20, 20, 20, 20, 11, 8, 11, 13, 13, 13, 1, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 20, 20, 20, 20, 20, 20, 20, 20, 20, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1] 21 rigid atoms, others: [48, 50, 49, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 92 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517747 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517747 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517747/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517747 Building REAL300004517748 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517748' /scratch/stefan/7774842/working/building/REAL300004517748 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517748 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517748/0 /scratch/stefan/7774842/working/building/REAL300004517748 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 789) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/789 `/scratch/stefan/7774842/working/3D/789' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC=C(C(=O)[O-])C=C1) `REAL300004517748.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517748/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517748 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 61 conformations in input total number of sets (complete confs): 61 using faster count positions algorithm for large data unique positions, atoms: [56, 56, 35, 56, 56, 57, 26, 12, 5, 12, 20, 21, 21, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 56, 56, 56, 56, 56, 57, 57, 57, 57, 57, 35, 35, 26, 26, 20, 20, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1] 61 rigid atoms, others: [48, 50, 49, 13, 47, 16, 17, 18, 19, 20, 21, 22, 23, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 313 number of broken/clashed sets: 61 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517748 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517748 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517748/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517748 Building REAL300004517749 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517749' /scratch/stefan/7774842/working/building/REAL300004517749 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517749 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517749/0 /scratch/stefan/7774842/working/building/REAL300004517749 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 790) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/790 `/scratch/stefan/7774842/working/3D/790' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)[C@H]1CC[C@@H](C(=O)[O-])C1) `REAL300004517749.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517749/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517749 none CC[NH+](CC)CCN(CC(C)C)C(=O)[C@H]1CC[C@@H](C(=O)[O-])C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 10, 9, 6, 4, 6, 6, 6, 6, 1, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 9, 9, 9, 9, 9, 10, 10, 10, 10, 10, 9, 9, 9, 9, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1] 10 rigid atoms, others: [48, 50, 51, 49, 13, 15, 16, 17, 18, 19, 20, 21, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 44 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517749 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517749 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517749/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517749 Building REAL300004517750 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517750' /scratch/stefan/7774842/working/building/REAL300004517750 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517750 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517750/0 /scratch/stefan/7774842/working/building/REAL300004517750 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 791) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/791 `/scratch/stefan/7774842/working/3D/791' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC=CC(CC(=O)[O-])=C1) `REAL300004517750.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517750 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC=CC(CC(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 52 conformations in input total number of sets (complete confs): 52 using faster count positions algorithm for large data unique positions, atoms: [47, 46, 34, 46, 46, 48, 29, 18, 6, 18, 23, 23, 23, 1, 6, 1, 1, 1, 1, 1, 1, 2, 6, 6, 1, 47, 47, 47, 47, 47, 48, 48, 48, 48, 48, 34, 34, 29, 29, 23, 23, 23, 23, 23, 23, 23, 23, 23, 1, 1, 1, 2, 2, 1] 52 rigid atoms, others: [48, 50, 49, 13, 15, 16, 17, 18, 19, 20, 53, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 51, 52]) total number of confs: 270 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517750 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517750 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517750/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517750 Building REAL300004517751 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517751' /scratch/stefan/7774842/working/building/REAL300004517751 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517751 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517751/0 /scratch/stefan/7774842/working/building/REAL300004517751 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 792) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/792 `/scratch/stefan/7774842/working/3D/792' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1=C(CC(=O)[O-])OC=C1) `REAL300004517751.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517751/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517751 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1=C(CC(=O)[O-])OC=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 5, 1, 11, 11, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 6, 6, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 3, 5, 5, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1] 6 rigid atoms, others: [49, 13, 15, 16, 17, 50, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 39 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517751 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517751 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517751/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517751 Building REAL300004517752 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517752' /scratch/stefan/7774842/working/building/REAL300004517752 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517752 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517752/0 /scratch/stefan/7774842/working/building/REAL300004517752 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 793) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/793 `/scratch/stefan/7774842/working/3D/793' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1=C(CC(=O)[O-])OC=C1C) `REAL300004517752.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517752/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517752 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1=C(CC(=O)[O-])OC=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 5, 1, 11, 11, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 6, 6, 6, 7, 5, 2, 2, 3, 3, 3, 3, 1, 2, 1, 1, 1, 2, 4, 4, 1, 1, 1, 1, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 6, 6, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 1, 2, 2, 2] 7 rigid atoms, others: [13, 15, 16, 17, 50, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53]) total number of confs: 52 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517752 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517752 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517752/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517752 Building REAL300004517753 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517753' /scratch/stefan/7774842/working/building/REAL300004517753 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517753 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517753/0 /scratch/stefan/7774842/working/building/REAL300004517753 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 794) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/794 `/scratch/stefan/7774842/working/3D/794' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC(C(=O)[O-])=CC=N1) `REAL300004517753.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517753/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517753 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC(C(=O)[O-])=CC=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 38, 38, 36, 38, 38, 38, 18, 8, 18, 25, 25, 25, 1, 8, 1, 1, 1, 1, 2, 2, 1, 1, 1, 41, 41, 41, 41, 41, 38, 38, 38, 38, 38, 38, 38, 38, 38, 25, 25, 25, 25, 25, 25, 25, 25, 25, 1, 1, 1] 41 rigid atoms, others: [48, 49, 13, 47, 16, 17, 18, 21, 22, 23, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 199 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517753 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517753 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517753/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517753 Building REAL300004517754 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517754' /scratch/stefan/7774842/working/building/REAL300004517754 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517754 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517754/0 /scratch/stefan/7774842/working/building/REAL300004517754 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 795) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/795 `/scratch/stefan/7774842/working/3D/795' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)CC1CCC(C(=O)[O-])CC1) `REAL300004517754.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517754.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517754/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517754 none CC[NH+](CC)CCN(CC(C)C)C(=O)CC1CCC(C(=O)[O-])CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 133 conformations in input total number of sets (complete confs): 133 using faster count positions algorithm for large data unique positions, atoms: [127, 125, 85, 125, 125, 127, 69, 47, 18, 47, 66, 66, 66, 5, 18, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 127, 127, 127, 127, 127, 127, 127, 127, 127, 127, 85, 85, 69, 69, 66, 66, 66, 66, 66, 66, 66, 66, 66, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 133 rigid atoms, others: [19, 56, 57, 55, 18, 15, 16, 17, 50, 51, 52, 53, 54, 23, 24, 20, 58, 59] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 692 number of broken/clashed sets: 133 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517754 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517754 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517754/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517754 Building REAL300004517755 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517755' /scratch/stefan/7774842/working/building/REAL300004517755 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517755 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517755/0 /scratch/stefan/7774842/working/building/REAL300004517755 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 796) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/796 `/scratch/stefan/7774842/working/3D/796' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)CC(C)(C)CC(=O)[O-]) `REAL300004517755.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517755.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517755/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.0.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.0.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.0.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517755 none CC[NH+](CC)CCN(CC(C)C)C(=O)CC(C)(C)CC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [7, 6, 6, 6, 6, 8, 5, 1, 1, 1, 3, 4, 4, 1, 3, 3, 5, 11, 11, 11, 12, 13, 13, 7, 7, 7, 7, 7, 8, 8, 8, 8, 8, 6, 6, 5, 5, 3, 3, 4, 4, 4, 4, 4, 4, 4, 5, 5, 11, 11, 11, 11, 11, 11, 12, 12] 16 rigid atoms, others: [8, 9, 13, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 107 number of broken/clashed sets: 16 ./output.0.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517755 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517755 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517755/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517755 Building REAL300004517756 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517756' /scratch/stefan/7774842/working/building/REAL300004517756 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517756 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517756/0 /scratch/stefan/7774842/working/building/REAL300004517756 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 797) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/797 `/scratch/stefan/7774842/working/3D/797' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)CC(C)CC(=O)[O-]) `REAL300004517756.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517756.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517756/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.0.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.0.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.0.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517756 none CC[NH+](CC)CCN(CC(C)C)C(=O)CC(C)CC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 5, 5, 5, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 31 conformations in input total number of sets (complete confs): 31 using default count positions algorithm for smaller data unique positions, atoms: [10, 7, 6, 7, 7, 11, 6, 1, 1, 1, 3, 3, 3, 1, 4, 4, 9, 10, 10, 12, 13, 13, 10, 10, 10, 10, 10, 11, 11, 11, 11, 11, 6, 6, 6, 6, 3, 3, 3, 3, 3, 3, 3, 3, 3, 9, 9, 10, 10, 10, 10, 12, 12] 31 rigid atoms, others: [8, 9, 13, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 127 number of broken/clashed sets: 31 ./output.0.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517756 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517756 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517756/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517756 Building REAL300004517757 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517757' /scratch/stefan/7774842/working/building/REAL300004517757 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517757 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517757/0 /scratch/stefan/7774842/working/building/REAL300004517757 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 798) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/798 `/scratch/stefan/7774842/working/3D/798' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC=NC2=C(C(=O)[O-])C=NN21) `REAL300004517757.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517757 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC=NC2=C(C(=O)[O-])C=NN21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 71 conformations in input total number of sets (complete confs): 71 using faster count positions algorithm for large data unique positions, atoms: [66, 61, 30, 61, 61, 67, 27, 15, 6, 15, 17, 19, 19, 1, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 66, 66, 66, 66, 66, 67, 67, 67, 67, 67, 30, 30, 27, 27, 17, 17, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1] 71 rigid atoms, others: [19, 18, 13, 15, 16, 17, 50, 51, 20, 21, 24, 25, 26, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 357 number of broken/clashed sets: 71 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517757 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517757 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517757/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517757 Building REAL300004517758 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517758' /scratch/stefan/7774842/working/building/REAL300004517758 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517758 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517758/0 /scratch/stefan/7774842/working/building/REAL300004517758 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 799) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/799 `/scratch/stefan/7774842/working/3D/799' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1=C(CC(=O)[O-])C2=CC=CC=C2N1) `REAL300004517758.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517758.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517758/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517758 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1=C(CC(=O)[O-])C2=CC=CC=C2N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 11, 23, 23, 23, 11, 7, 6, 7, 7, 7, 7, 1, 6, 1, 1, 1, 2, 6, 6, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 11, 11, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 1, 1, 1, 1, 1] 23 rigid atoms, others: [54, 57, 55, 13, 15, 16, 17, 56, 21, 22, 23, 24, 25, 26, 27, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 122 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517758 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517758 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517758/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517758 Building REAL300004517759 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517759' /scratch/stefan/7774842/working/building/REAL300004517759 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517759 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517759/0 /scratch/stefan/7774842/working/building/REAL300004517759 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 800) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/800 `/scratch/stefan/7774842/working/3D/800' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1=NOC(C(=O)[O-])=C1) `REAL300004517759.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517759.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517759/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517759 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1=NOC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 8, 12, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [60, 54, 53, 54, 54, 60, 52, 32, 12, 32, 40, 40, 40, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 60, 60, 60, 60, 60, 60, 60, 60, 60, 60, 53, 53, 52, 52, 40, 40, 40, 40, 40, 40, 40, 40, 40, 1] 66 rigid atoms, others: [13, 46, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 317 number of broken/clashed sets: 66 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517759 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517759 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517759/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517759 Building REAL300004517760 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517760' /scratch/stefan/7774842/working/building/REAL300004517760 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517760 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517760/0 /scratch/stefan/7774842/working/building/REAL300004517760 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 801) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/801 `/scratch/stefan/7774842/working/3D/801' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)CC1CCCC2=CC=C(C(=O)[O-])C=C21) `REAL300004517760.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517760.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517760/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517760 none CC[NH+](CC)CCN(CC(C)C)C(=O)CC1CCCC2=CC=C(C(=O)[O-])C=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 24 conformations in input total number of sets (complete confs): 24 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 21, 23, 23, 24, 21, 16, 9, 16, 19, 19, 19, 4, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 24, 24, 24, 24, 24, 21, 21, 21, 21, 19, 19, 19, 19, 19, 19, 19, 19, 19, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 24 rigid atoms, others: [15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 114 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517760 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517760 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517760/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517760 Building REAL300004517761 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517761' /scratch/stefan/7774842/working/building/REAL300004517761 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517761 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517761/0 /scratch/stefan/7774842/working/building/REAL300004517761 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 802) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/802 `/scratch/stefan/7774842/working/3D/802' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1=C(C)OC(C(=O)[O-])=C1) `REAL300004517761.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517761 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1=C(C)OC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 5, 12, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 25 conformations in input total number of sets (complete confs): 25 using default count positions algorithm for smaller data unique positions, atoms: [23, 21, 21, 21, 21, 23, 20, 11, 8, 11, 14, 14, 14, 1, 8, 1, 1, 1, 1, 1, 1, 2, 2, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 21, 21, 20, 20, 14, 14, 14, 14, 14, 14, 14, 14, 14, 2, 2, 2, 1] 25 rigid atoms, others: [50, 13, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 129 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517761 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517761 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517761/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517761 Building REAL300004517762 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517762' /scratch/stefan/7774842/working/building/REAL300004517762 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517762 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517762/0 /scratch/stefan/7774842/working/building/REAL300004517762 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 803) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/803 `/scratch/stefan/7774842/working/3D/803' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC(C)=C(C(=O)[O-])O1) `REAL300004517762.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517762 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC(C)=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 1, 5, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [28, 21, 18, 21, 21, 23, 18, 10, 6, 10, 10, 10, 10, 1, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 28, 28, 28, 28, 28, 23, 23, 23, 23, 23, 18, 18, 18, 18, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 2, 2, 2] 30 rigid atoms, others: [13, 47, 16, 17, 18, 19, 20, 23, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50]) total number of confs: 146 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517762 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517762 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517762/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517762 Building REAL300004517763 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517763' /scratch/stefan/7774842/working/building/REAL300004517763 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517763 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517763/0 /scratch/stefan/7774842/working/building/REAL300004517763 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 804) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/804 `/scratch/stefan/7774842/working/3D/804' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)CN1C=C(C(=O)[O-])C=N1) `REAL300004517763.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517763/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517763 none CC[NH+](CC)CCN(CC(C)C)C(=O)CN1C=C(C(=O)[O-])C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 5, 8, 1, 1, 1, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 11, 14, 14, 14, 11, 11, 7, 11, 11, 11, 11, 5, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 5, 5, 1, 1] 14 rigid atoms, others: [49, 50, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 54 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517763 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517763 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517763/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517763 Building REAL300004517764 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517764' /scratch/stefan/7774842/working/building/REAL300004517764 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517764 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517764/0 /scratch/stefan/7774842/working/building/REAL300004517764 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 805) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/805 `/scratch/stefan/7774842/working/3D/805' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC=C(C=CC(=O)[O-])O1) `REAL300004517764.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517764.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517764/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517764 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC=C(C=CC(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [38, 32, 17, 32, 32, 34, 14, 12, 6, 12, 17, 17, 17, 1, 6, 1, 1, 1, 1, 1, 6, 6, 14, 14, 1, 38, 38, 38, 38, 38, 34, 34, 34, 34, 34, 17, 17, 14, 14, 17, 17, 17, 17, 17, 17, 17, 17, 17, 1, 1, 6, 6] 45 rigid atoms, others: [48, 49, 13, 15, 16, 17, 18, 19, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 50, 51]) total number of confs: 244 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517764 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517764 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517764/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517764 Building REAL300004517765 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517765' /scratch/stefan/7774842/working/building/REAL300004517765 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517765 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517765/0 /scratch/stefan/7774842/working/building/REAL300004517765 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 806) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/806 `/scratch/stefan/7774842/working/3D/806' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC=C(OCC(=O)[O-])C=C1) `REAL300004517765.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517765.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517765/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517765 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC=C(OCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [14, 13, 8, 13, 13, 14, 8, 5, 4, 5, 9, 9, 9, 1, 4, 1, 1, 1, 1, 1, 5, 5, 6, 6, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 8, 8, 8, 8, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 5, 5, 1, 1] 20 rigid atoms, others: [50, 17, 13, 15, 16, 49, 18, 19, 53, 54, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 51, 52]) total number of confs: 91 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517765 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517765 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517765/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517765 Building REAL300004517766 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517766' /scratch/stefan/7774842/working/building/REAL300004517766 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517766 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517766/0 /scratch/stefan/7774842/working/building/REAL300004517766 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 807) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/807 `/scratch/stefan/7774842/working/3D/807' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)CCSCC(=O)[O-]) `REAL300004517766.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517766.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517766/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.0.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.0.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.0.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517766 none CC[NH+](CC)CCN(CC(C)C)C(=O)CCSCC(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 5, 5, 14, 5, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [13, 10, 6, 10, 10, 15, 5, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 5, 7, 9, 9, 9, 13, 13, 13, 13, 13, 15, 15, 15, 15, 15, 6, 6, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 5, 5, 9, 9] 19 rigid atoms, others: [8, 9, 13, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 130 number of broken/clashed sets: 19 ./output.0.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517766 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517766 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517766/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517766 Building REAL300004517767 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517767' /scratch/stefan/7774842/working/building/REAL300004517767 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517767 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517767/0 /scratch/stefan/7774842/working/building/REAL300004517767 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 808) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/808 `/scratch/stefan/7774842/working/3D/808' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC=C(C(=O)[O-])C=N1) `REAL300004517767.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517767.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517767/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517767 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC=C(C(=O)[O-])C=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [18, 17, 13, 17, 17, 18, 10, 7, 5, 7, 9, 9, 9, 1, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 13, 13, 10, 10, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1] 20 rigid atoms, others: [48, 49, 13, 47, 16, 17, 18, 19, 20, 21, 22, 23, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 100 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517767 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517767 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517767/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517767 Building REAL300004517768 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517768' /scratch/stefan/7774842/working/building/REAL300004517768 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517768 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517768/0 /scratch/stefan/7774842/working/building/REAL300004517768 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 809) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/809 `/scratch/stefan/7774842/working/3D/809' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC(C(=O)[O-])=NN1C) `REAL300004517768.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517768.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517768/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517768 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC(C(=O)[O-])=NN1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 11, 11, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [19, 16, 16, 16, 16, 18, 16, 7, 5, 7, 10, 10, 10, 1, 5, 1, 1, 1, 1, 2, 2, 1, 1, 1, 19, 19, 19, 19, 19, 18, 18, 18, 18, 18, 16, 16, 16, 16, 10, 10, 10, 10, 10, 10, 10, 10, 10, 1, 2, 2, 2] 21 rigid atoms, others: [13, 47, 16, 17, 18, 21, 22, 23, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50]) total number of confs: 122 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517768 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517768 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517768/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517768 Building REAL300004517769 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517769' /scratch/stefan/7774842/working/building/REAL300004517769 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517769 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517769/0 /scratch/stefan/7774842/working/building/REAL300004517769 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 810) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/810 `/scratch/stefan/7774842/working/3D/810' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)[C@H]1C[C@@H](C)[C@H](C(=O)[O-])O1) `REAL300004517769.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517769.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517769/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517769 none CC[NH+](CC)CCN(CC(C)C)C(=O)[C@H]1C[C@@H](C)[C@H](C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 7, 5, 5, 7, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 19 conformations in input total number of sets (complete confs): 19 using default count positions algorithm for smaller data unique positions, atoms: [17, 13, 11, 13, 13, 16, 11, 6, 4, 6, 6, 6, 6, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 17, 17, 17, 17, 17, 16, 16, 16, 16, 16, 11, 11, 11, 11, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 2, 2, 2] 19 rigid atoms, others: [19, 50, 13, 15, 16, 17, 18, 51, 20, 21, 22, 23, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 52, 53, 54]) total number of confs: 104 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517769 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517769 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517769/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517769 Building REAL300004517770 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517770' /scratch/stefan/7774842/working/building/REAL300004517770 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517770 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517770/0 /scratch/stefan/7774842/working/building/REAL300004517770 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 811) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/811 `/scratch/stefan/7774842/working/3D/811' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC=C(CC(=O)[O-])C=C1) `REAL300004517770.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517770 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC=C(CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [29, 28, 22, 28, 28, 29, 21, 13, 5, 13, 19, 19, 19, 1, 5, 1, 1, 1, 1, 1, 3, 5, 5, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 22, 22, 21, 21, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 3, 3, 1, 1] 34 rigid atoms, others: [48, 49, 13, 15, 16, 17, 18, 19, 52, 53, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 50, 51]) total number of confs: 171 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517770 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517770 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517770/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517770 Building REAL300004517771 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517771' /scratch/stefan/7774842/working/building/REAL300004517771 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517771 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517771/0 /scratch/stefan/7774842/working/building/REAL300004517771 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 812) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/812 `/scratch/stefan/7774842/working/3D/812' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC=C(C=CC(=O)[O-])C=C1) `REAL300004517771.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517771.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517771/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517771 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC=C(C=CC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [79, 72, 35, 72, 72, 77, 24, 12, 5, 12, 19, 19, 19, 1, 5, 1, 1, 1, 1, 1, 5, 5, 13, 13, 1, 1, 79, 79, 79, 79, 79, 77, 77, 77, 77, 77, 35, 35, 24, 24, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 5, 5, 1, 1] 143 rigid atoms, others: [50, 17, 13, 15, 16, 49, 18, 19, 53, 54, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 51, 52]) total number of confs: 470 number of broken/clashed sets: 143 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517771 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517771 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517771/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517771 Building REAL300004517772 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517772' /scratch/stefan/7774842/working/building/REAL300004517772 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517772 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517772/0 /scratch/stefan/7774842/working/building/REAL300004517772 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 813) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/813 `/scratch/stefan/7774842/working/3D/813' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C=CC1=CC(C(=O)[O-])=CO1) `REAL300004517772.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517772/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517772 none CC[NH+](CC)CCN(CC(C)C)C(=O)C=CC1=CC(C(=O)[O-])=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 187 conformations in input total number of sets (complete confs): 187 using faster count positions algorithm for large data unique positions, atoms: [181, 180, 137, 180, 180, 182, 115, 71, 35, 71, 96, 96, 96, 6, 34, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 181, 181, 181, 181, 181, 182, 182, 182, 182, 182, 137, 137, 115, 115, 96, 96, 96, 96, 96, 96, 96, 96, 96, 6, 6, 1, 1] 187 rigid atoms, others: [51, 50, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 966 number of broken/clashed sets: 187 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517772 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517772 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517772/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517772 Building REAL300004517773 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517773' /scratch/stefan/7774842/working/building/REAL300004517773 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517773 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517773/0 /scratch/stefan/7774842/working/building/REAL300004517773 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 814) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/814 `/scratch/stefan/7774842/working/3D/814' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)COCC1=C(C(=O)[O-])N=CO1) `REAL300004517773.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517773.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517773/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517773 none CC[NH+](CC)CCN(CC(C)C)C(=O)COCC1=C(C(=O)[O-])N=CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 5, 12, 5, 1, 1, 1, 11, 11, 8, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 6 conformations in input total number of sets (complete confs): 6 using default count positions algorithm for smaller data unique positions, atoms: [6, 6, 5, 6, 6, 6, 5, 5, 5, 5, 5, 5, 5, 4, 5, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 4, 4, 2, 2, 1] 6 rigid atoms, others: [17, 18, 19, 20, 21, 22, 23, 24, 25, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 20 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517773 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517773 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517773/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517773 Building REAL300004517774 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517774' /scratch/stefan/7774842/working/building/REAL300004517774 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517774 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517774/0 /scratch/stefan/7774842/working/building/REAL300004517774 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 815) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/815 `/scratch/stefan/7774842/working/3D/815' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C=CC1=CC=C(C(=O)[O-])O1) `REAL300004517774.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517774.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517774/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517774 none CC[NH+](CC)CCN(CC(C)C)C(=O)C=CC1=CC=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 59 conformations in input total number of sets (complete confs): 59 using faster count positions algorithm for large data unique positions, atoms: [59, 58, 49, 58, 58, 59, 46, 31, 15, 31, 39, 39, 39, 4, 14, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 59, 59, 59, 59, 59, 59, 59, 59, 59, 59, 49, 49, 46, 46, 39, 39, 39, 39, 39, 39, 39, 39, 39, 4, 4, 1, 1] 59 rigid atoms, others: [51, 50, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 297 number of broken/clashed sets: 59 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517774 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517774 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517774/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517774 Building REAL300004517775 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517775' /scratch/stefan/7774842/working/building/REAL300004517775 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517775 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517775/0 /scratch/stefan/7774842/working/building/REAL300004517775 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 816) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/816 `/scratch/stefan/7774842/working/3D/816' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)[C@H]1CC[C@@H](C(=O)[O-])C1) `REAL300004517775.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517775/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517775 none CC[NH+](CC)CCN(CC(C)C)C(=O)[C@H]1CC[C@@H](C(=O)[O-])C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [9, 9, 9, 9, 9, 10, 9, 6, 4, 6, 6, 6, 6, 1, 4, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 9, 9, 9, 9, 9, 10, 10, 10, 10, 10, 9, 9, 9, 9, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1] 10 rigid atoms, others: [48, 50, 51, 49, 13, 15, 16, 17, 18, 19, 20, 21, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 44 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517775 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517775 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517775/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517775 Building REAL300004517776 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517776' /scratch/stefan/7774842/working/building/REAL300004517776 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517776 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517776/0 /scratch/stefan/7774842/working/building/REAL300004517776 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 817) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/817 `/scratch/stefan/7774842/working/3D/817' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC=C(C)C(C(=O)[O-])=C1) `REAL300004517776.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517776/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517776 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC=C(C)C(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 5, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 11, 9, 11, 11, 11, 8, 6, 5, 6, 6, 6, 6, 1, 5, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 9, 9, 8, 8, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 2, 2, 2, 1] 11 rigid atoms, others: [48, 49, 13, 15, 16, 17, 18, 19, 20, 21, 24, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 50, 51, 52]) total number of confs: 55 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517776 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517776 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517776/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517776 Building REAL300004517777 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517777' /scratch/stefan/7774842/working/building/REAL300004517777 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517777 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517777/0 /scratch/stefan/7774842/working/building/REAL300004517777 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 818) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/818 `/scratch/stefan/7774842/working/3D/818' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CN=CC(C(=O)[O-])=C1) `REAL300004517777.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517777.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517777/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517777 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CN=CC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 8, 1, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [21, 20, 20, 20, 20, 20, 20, 11, 8, 11, 13, 13, 13, 1, 8, 1, 1, 1, 1, 1, 1, 2, 2, 1, 21, 21, 21, 21, 21, 20, 20, 20, 20, 20, 20, 20, 20, 20, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 1, 1] 21 rigid atoms, others: [48, 49, 13, 47, 16, 17, 18, 19, 20, 23, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 96 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517777 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517777 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517777/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517777 Building REAL300004517778 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517778' /scratch/stefan/7774842/working/building/REAL300004517778 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517778 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517778/0 /scratch/stefan/7774842/working/building/REAL300004517778 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 819) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/819 `/scratch/stefan/7774842/working/3D/819' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC(C(=O)[O-])=CN=C1C) `REAL300004517778.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517778.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517778/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517778 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC(C(=O)[O-])=CN=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 11, 11, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 16 conformations in input total number of sets (complete confs): 16 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 16, 16, 16, 7, 5, 7, 8, 8, 8, 1, 5, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 8, 8, 8, 8, 8, 8, 8, 8, 8, 1, 1, 2, 2, 2] 16 rigid atoms, others: [48, 49, 13, 15, 16, 17, 18, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 50, 51, 52]) total number of confs: 77 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517778 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517778 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517778/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517778 Building REAL300004517779 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517779' /scratch/stefan/7774842/working/building/REAL300004517779 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517779 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517779/0 /scratch/stefan/7774842/working/building/REAL300004517779 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 820) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/820 `/scratch/stefan/7774842/working/3D/820' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)CN1C=CC(C(=O)[O-])=N1) `REAL300004517779.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517779.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517779/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517779 none CC[NH+](CC)CCN(CC(C)C)C(=O)CN1C=CC(C(=O)[O-])=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 5, 8, 1, 1, 1, 1, 11, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 20, 13, 20, 20, 20, 13, 12, 9, 12, 12, 12, 12, 7, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 13, 13, 13, 13, 12, 12, 12, 12, 12, 12, 12, 12, 12, 7, 7, 1, 1] 20 rigid atoms, others: [49, 50, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 88 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517779 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517779 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517779/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517779 Building REAL300004517780 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517780' /scratch/stefan/7774842/working/building/REAL300004517780 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517780 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517780/0 /scratch/stefan/7774842/working/building/REAL300004517780 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 821) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/821 `/scratch/stefan/7774842/working/3D/821' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)CCCN1C=CC(C(=O)[O-])=N1) `REAL300004517780.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517780.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517780/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517780 none CC[NH+](CC)CCN(CC(C)C)C(=O)CCCN1C=CC(C(=O)[O-])=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 5, 5, 5, 8, 1, 1, 1, 1, 11, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [7, 7, 7, 7, 7, 7, 7, 4, 3, 4, 4, 4, 4, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 3, 3, 3, 3, 1, 1] 7 rigid atoms, others: [17, 18, 19, 20, 21, 22, 55, 56, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 33 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517780 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517780 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517780/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517780 Building REAL300004517781 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517781' /scratch/stefan/7774842/working/building/REAL300004517781 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517781 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517781/0 /scratch/stefan/7774842/working/building/REAL300004517781 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 822) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/822 `/scratch/stefan/7774842/working/3D/822' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)[C@H]1CC[C@@H](CCC(=O)[O-])O1) `REAL300004517781.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517781 none CC[NH+](CC)CCN(CC(C)C)C(=O)[C@H]1CC[C@@H](CCC(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 7, 5, 5, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 3, 3, 3, 4, 3, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 5, 5, 5, 5] 7 rigid atoms, others: [19, 50, 13, 15, 16, 17, 18, 51, 52, 53, 20, 26, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 54, 55, 56, 57]) total number of confs: 38 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517781 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517781 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517781/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517781 Building REAL300004517782 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517782' /scratch/stefan/7774842/working/building/REAL300004517782 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517782 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517782/0 /scratch/stefan/7774842/working/building/REAL300004517782 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 823) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/823 `/scratch/stefan/7774842/working/3D/823' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)CC[C@@H]1C[C@H](C(=O)[O-])CO1) `REAL300004517782.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517782/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517782 none CC[NH+](CC)CCN(CC(C)C)C(=O)CC[C@@H]1C[C@H](C(=O)[O-])CO1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 5, 5, 5, 7, 5, 5, 7, 1, 11, 11, 5, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [33, 30, 27, 30, 30, 34, 25, 15, 14, 15, 18, 18, 18, 10, 14, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 33, 33, 33, 33, 33, 34, 34, 34, 34, 34, 27, 27, 25, 25, 18, 18, 18, 18, 18, 18, 18, 18, 18, 10, 10, 7, 7, 1, 1, 1, 1] 37 rigid atoms, others: [22, 57, 16, 17, 18, 19, 20, 21, 54, 55, 56, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 205 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517782 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517782 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517782/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517782 Building REAL300004517783 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517783' /scratch/stefan/7774842/working/building/REAL300004517783 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517783 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517783/0 /scratch/stefan/7774842/working/building/REAL300004517783 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 824) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/824 `/scratch/stefan/7774842/working/3D/824' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1=C(C)C=C(C(=O)[O-])O1) `REAL300004517783.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517783.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517783/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517783 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1=C(C)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 5, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 34 conformations in input total number of sets (complete confs): 34 using default count positions algorithm for smaller data unique positions, atoms: [31, 30, 30, 30, 30, 33, 30, 15, 6, 15, 18, 18, 18, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31, 33, 33, 33, 33, 33, 30, 30, 30, 30, 18, 18, 18, 18, 18, 18, 18, 18, 18, 2, 2, 2, 1] 34 rigid atoms, others: [50, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 160 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517783 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517783 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517783/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517783 Building REAL300004517784 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517784' /scratch/stefan/7774842/working/building/REAL300004517784 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517784 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517784/0 /scratch/stefan/7774842/working/building/REAL300004517784 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 825) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/825 `/scratch/stefan/7774842/working/3D/825' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)[C@@H]1C2C=CC(CC2)[C@@H]1C(=O)[O-]) `REAL300004517784.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517784.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517784/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517784 none CC[NH+](CC)CCN(CC(C)C)C(=O)[C@@H]1C2C=CC(CC2)[C@@H]1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 5, 7, 5, 1, 1, 5, 5, 5, 5, 7, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1] 3 rigid atoms, others: [19, 25, 54, 57, 55, 24, 13, 15, 16, 17, 18, 51, 52, 53, 22, 23, 56, 20, 58, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 15 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517784 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517784 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517784/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517784 Building REAL300004517785 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517785' /scratch/stefan/7774842/working/building/REAL300004517785 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517785 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517785/0 /scratch/stefan/7774842/working/building/REAL300004517785 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 826) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/826 `/scratch/stefan/7774842/working/3D/826' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C(C(=O)[O-])C(C)C) `REAL300004517785.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517785.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517785/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.0.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.0.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.0.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517785 none CC[NH+](CC)CCN(CC(C)C)C(=O)C(C(=O)[O-])C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 5, 5, 5, 7, 5, 1, 1, 1, 4, 4, 4, 1, 4, 4, 4, 4, 4, 4, 4, 4, 8, 8, 8, 8, 8, 7, 7, 7, 7, 7, 5, 5, 5, 5, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4] 12 rigid atoms, others: [8, 9, 13, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 63 number of broken/clashed sets: 12 ./output.0.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517785 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517785 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517785/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517785 Building REAL300004517786 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517786' /scratch/stefan/7774842/working/building/REAL300004517786 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517786 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517786/0 /scratch/stefan/7774842/working/building/REAL300004517786 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 827) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/827 `/scratch/stefan/7774842/working/3D/827' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)[C@H]1CCCC[C@H]1C(=O)[O-]) `REAL300004517786.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517786.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517786/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517786 none CC[NH+](CC)CCN(CC(C)C)C(=O)[C@H]1CCCC[C@H]1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 5, 5, 5, 7, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1] 5 rigid atoms, others: [51, 50, 22, 49, 23, 13, 15, 16, 17, 18, 19, 52, 21, 54, 55, 56, 20, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 20 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517786 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517786 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517786/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517786 Building REAL300004517787 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517787' /scratch/stefan/7774842/working/building/REAL300004517787 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004517787 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517787/0 /scratch/stefan/7774842/working/building/REAL300004517787 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 828) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/828 `/scratch/stefan/7774842/working/3D/828' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C[N@@H+]1CCCC(C(=O)[O-])C1) `REAL300004517787.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517787/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517787 none CC[NH+](CC)CCN(CC(C)C)C(=O)C[N@@H+]1CCCC(C(=O)[O-])C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 5, 9, 6, 5, 5, 5, 5, 1, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [14, 13, 12, 13, 13, 14, 11, 8, 5, 8, 10, 10, 10, 3, 5, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 12, 12, 11, 11, 10, 10, 10, 10, 10, 10, 10, 10, 10, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 15 rigid atoms, others: [51, 22, 57, 15, 16, 17, 18, 19, 52, 53, 54, 55, 56, 25, 58, 59, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 87 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517787 /scratch/stefan/7774842/working /scratch/stefan/7774842 mkdir: created directory `1' /scratch/stefan/7774842/working/building/REAL300004517787/1 /scratch/stefan/7774842/working/building/REAL300004517787 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 1 (index: 829) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/829 `/scratch/stefan/7774842/working/3D/829' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C[N@H+]1CCCC(C(=O)[O-])C1) `REAL300004517787.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004517787.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517787/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.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: REAL300004517787 none CC[NH+](CC)CCN(CC(C)C)C(=O)C[N@H+]1CCCC(C(=O)[O-])C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 5, 9, 6, 5, 5, 5, 5, 1, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [12, 12, 12, 12, 12, 12, 11, 7, 6, 7, 8, 8, 8, 3, 6, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11, 11, 8, 8, 8, 8, 8, 8, 8, 8, 8, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 12 rigid atoms, others: [51, 22, 57, 15, 16, 17, 18, 19, 52, 53, 54, 55, 56, 25, 58, 59, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 58 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517787 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517787 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 1: /scratch/stefan/7774842/working/building/REAL300004517787/1.* 0: /scratch/stefan/7774842/working/building/REAL300004517787/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517787 Building REAL300004517788 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517788' /scratch/stefan/7774842/working/building/REAL300004517788 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517788 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517788/0 /scratch/stefan/7774842/working/building/REAL300004517788 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 830) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/830 `/scratch/stefan/7774842/working/3D/830' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1=C(CC(=O)[O-])C2=CC=CC=C2N1) `REAL300004517788.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517788.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517788/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517788 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1=C(CC(=O)[O-])C2=CC=CC=C2N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [23, 23, 11, 23, 23, 23, 11, 7, 6, 7, 7, 7, 7, 1, 6, 1, 1, 1, 2, 6, 6, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 11, 11, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 1, 1, 1, 1, 1] 23 rigid atoms, others: [54, 57, 55, 13, 15, 16, 17, 56, 21, 22, 23, 24, 25, 26, 27, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 122 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517788 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517788 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517788/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517788 Building REAL300004517789 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517789' /scratch/stefan/7774842/working/building/REAL300004517789 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517789 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517789/0 /scratch/stefan/7774842/working/building/REAL300004517789 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 831) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/831 `/scratch/stefan/7774842/working/3D/831' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)CN1C=C(C(=O)[O-])C2=CC=CC=C21) `REAL300004517789.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517789.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517789/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517789 none CC[NH+](CC)CCN(CC(C)C)C(=O)CN1C=C(C(=O)[O-])C2=CC=CC=C21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 5, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 10 conformations in input total number of sets (complete confs): 10 using default count positions algorithm for smaller data unique positions, atoms: [10, 10, 6, 10, 10, 10, 6, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 6, 6, 6, 6, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1] 10 rigid atoms, others: [54, 57, 55, 15, 16, 17, 18, 19, 56, 53, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 20, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 53 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517789 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517789 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517789/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517789 Building REAL300004517790 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517790' /scratch/stefan/7774842/working/building/REAL300004517790 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517790 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517790/0 /scratch/stefan/7774842/working/building/REAL300004517790 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 832) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/832 `/scratch/stefan/7774842/working/3D/832' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1CC2(CC2C(=O)[O-])C1) `REAL300004517790.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517790/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517790 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1CC2(CC2C(=O)[O-])C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [50, 48, 25, 48, 48, 51, 20, 14, 8, 14, 16, 17, 17, 1, 8, 1, 1, 1, 1, 1, 1, 3, 3, 1, 50, 50, 50, 50, 50, 51, 51, 51, 51, 51, 25, 25, 20, 20, 16, 16, 17, 17, 17, 17, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1] 56 rigid atoms, others: [48, 50, 51, 49, 13, 47, 16, 17, 18, 19, 20, 53, 54, 23, 52, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 254 number of broken/clashed sets: 56 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517790 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517790 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517790/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517790 Building REAL300004517791 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517791' /scratch/stefan/7774842/working/building/REAL300004517791 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517791 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517791/0 /scratch/stefan/7774842/working/building/REAL300004517791 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 833) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/833 `/scratch/stefan/7774842/working/3D/833' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)[C@H]1C[C@]1(C(=O)[O-])C(C)C) `REAL300004517791.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517791/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517791 none CC[NH+](CC)CCN(CC(C)C)C(=O)[C@H]1C[C@]1(C(=O)[O-])C(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 9 conformations in input total number of sets (complete confs): 9 using default count positions algorithm for smaller data unique positions, atoms: [6, 5, 4, 5, 5, 7, 4, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 2, 2, 1, 5, 5, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 4, 4, 4, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 5, 5, 5, 5, 5, 5, 5] 9 rigid atoms, others: [48, 49, 13, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 50, 51, 52, 53, 54, 55, 56]) total number of confs: 57 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517791 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517791 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517791/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517791 Building REAL300004517792 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517792' /scratch/stefan/7774842/working/building/REAL300004517792 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517792 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517792/0 /scratch/stefan/7774842/working/building/REAL300004517792 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 834) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/834 `/scratch/stefan/7774842/working/3D/834' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC(C(=O)[O-])=CC=C1C) `REAL300004517792.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517792.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517792/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517792 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC(C(=O)[O-])=CC=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 14, 14, 14, 14, 14, 6, 4, 6, 7, 7, 7, 1, 4, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 1, 2, 2, 2] 14 rigid atoms, others: [48, 50, 49, 13, 15, 16, 17, 18, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 19, 20, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 51, 52, 53]) total number of confs: 69 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517792 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517792 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517792/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517792 Building REAL300004517793 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517793' /scratch/stefan/7774842/working/building/REAL300004517793 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517793 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517793/0 /scratch/stefan/7774842/working/building/REAL300004517793 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 835) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/835 `/scratch/stefan/7774842/working/3D/835' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1CC(C)(C(=O)[O-])C1) `REAL300004517793.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517793/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517793 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1CC(C)(C(=O)[O-])C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 5, 5, 5, 5, 1, 11, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 14 conformations in input total number of sets (complete confs): 14 using default count positions algorithm for smaller data unique positions, atoms: [12, 11, 7, 11, 11, 12, 6, 4, 3, 4, 5, 5, 5, 1, 3, 1, 1, 1, 1, 1, 3, 3, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 7, 7, 6, 6, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 2, 2, 2, 1, 1] 14 rigid atoms, others: [48, 13, 46, 15, 16, 17, 18, 19, 52, 53, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 49, 50, 51]) total number of confs: 74 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517793 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517793 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517793/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517793 Building REAL300004517794 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517794' /scratch/stefan/7774842/working/building/REAL300004517794 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517794 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517794/0 /scratch/stefan/7774842/working/building/REAL300004517794 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 836) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/836 `/scratch/stefan/7774842/working/3D/836' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC(C(=O)[O-])=NN1) `REAL300004517794.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517794/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517794 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC(C(=O)[O-])=NN1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 11, 11, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [10, 7, 7, 7, 7, 9, 7, 6, 6, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 9, 9, 9, 9, 9, 7, 7, 7, 7, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1] 12 rigid atoms, others: [13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 49 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517794 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517794 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517794/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517794 Building REAL300004517795 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517795' /scratch/stefan/7774842/working/building/REAL300004517795 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517795 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517795/0 /scratch/stefan/7774842/working/building/REAL300004517795 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 837) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/837 `/scratch/stefan/7774842/working/3D/837' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CN=CC(C(=O)[O-])=C1C) `REAL300004517795.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517795.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517795/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517795 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CN=CC(C(=O)[O-])=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 8, 1, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 12 conformations in input total number of sets (complete confs): 12 using default count positions algorithm for smaller data unique positions, atoms: [12, 11, 11, 11, 11, 12, 11, 7, 5, 7, 7, 7, 7, 1, 5, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 12, 12, 11, 11, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1, 1, 2, 2, 2] 12 rigid atoms, others: [48, 49, 13, 15, 16, 17, 18, 19, 20, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 50, 51, 52]) total number of confs: 60 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517795 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517795 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517795/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517795 Building REAL300004517796 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517796' /scratch/stefan/7774842/working/building/REAL300004517796 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517796 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517796/0 /scratch/stefan/7774842/working/building/REAL300004517796 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 838) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/838 `/scratch/stefan/7774842/working/3D/838' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C(=O)[O-])C(=O)N(CC[NH+](CC)CC)CC(C)C) `REAL300004517796.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.0.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.0.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.0.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517796 none CCCC(C(=O)[O-])C(=O)N(CC[NH+](CC)CC)CC(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 1, 11, 8, 5, 5, 9, 6, 5, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 7, 7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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: [7, 7, 4, 3, 4, 5, 5, 1, 3, 1, 1, 4, 4, 6, 6, 9, 6, 10, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 7, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 10, 10, 10, 10, 10, 2, 2, 2, 2, 2, 2, 2, 2, 2] 31 rigid atoms, others: [9, 10, 18, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 98 number of broken/clashed sets: 31 ./output.0.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517796 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517796 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517796/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517796 Building REAL300004517797 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517797' /scratch/stefan/7774842/working/building/REAL300004517797 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517797 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517797/0 /scratch/stefan/7774842/working/building/REAL300004517797 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 839) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/839 `/scratch/stefan/7774842/working/3D/839' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC=C(C(=O)[O-])C=C1C) `REAL300004517797.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517797/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517797 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 56 conformations in input total number of sets (complete confs): 56 using faster count positions algorithm for large data unique positions, atoms: [53, 53, 35, 53, 53, 54, 28, 14, 7, 14, 21, 21, 21, 1, 7, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 53, 53, 53, 53, 53, 54, 54, 54, 54, 54, 35, 35, 28, 28, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 2, 2, 2] 56 rigid atoms, others: [48, 50, 49, 13, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 51, 52, 53]) total number of confs: 302 number of broken/clashed sets: 56 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517797 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517797 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517797/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517797 Building REAL300004517798 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517798' /scratch/stefan/7774842/working/building/REAL300004517798 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517798 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517798/0 /scratch/stefan/7774842/working/building/REAL300004517798 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 840) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/840 `/scratch/stefan/7774842/working/3D/840' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC=C(C(=O)[O-])C=C1Cl) `REAL300004517798.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517798.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517798/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517798 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC=C(C(=O)[O-])C=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [28, 28, 19, 28, 28, 28, 17, 12, 6, 12, 15, 15, 15, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 19, 19, 17, 17, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1] 29 rigid atoms, others: [48, 50, 49, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 139 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517798 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517798 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517798/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517798 Building REAL300004517799 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517799' /scratch/stefan/7774842/working/building/REAL300004517799 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517799 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517799/0 /scratch/stefan/7774842/working/building/REAL300004517799 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 841) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/841 `/scratch/stefan/7774842/working/3D/841' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1CC2(CC(C(=O)[O-])C2)C1) `REAL300004517799.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517799 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1CC2(CC(C(=O)[O-])C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 62 conformations in input total number of sets (complete confs): 62 using faster count positions algorithm for large data unique positions, atoms: [57, 53, 35, 53, 53, 57, 29, 18, 7, 18, 20, 21, 21, 1, 7, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 57, 57, 57, 57, 57, 57, 57, 57, 57, 57, 35, 35, 29, 29, 20, 20, 21, 21, 21, 21, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 62 rigid atoms, others: [48, 18, 56, 51, 49, 57, 55, 13, 15, 16, 17, 50, 19, 52, 53, 54, 23, 24, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 296 number of broken/clashed sets: 62 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517799 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517799 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517799/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517799 Building REAL300004517800 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517800' /scratch/stefan/7774842/working/building/REAL300004517800 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517800 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517800/0 /scratch/stefan/7774842/working/building/REAL300004517800 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 842) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/842 `/scratch/stefan/7774842/working/3D/842' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC(OC)=CC(C(=O)[O-])=N1) `REAL300004517800.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517800.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517800/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517800 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC(OC)=CC(C(=O)[O-])=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [19, 18, 15, 18, 18, 19, 13, 11, 6, 11, 13, 13, 13, 1, 6, 1, 1, 1, 1, 2, 1, 1, 1, 2, 2, 1, 19, 19, 19, 19, 19, 19, 19, 19, 19, 19, 15, 15, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 13, 1, 2, 2, 2, 1] 20 rigid atoms, others: [17, 13, 15, 16, 49, 18, 20, 21, 22, 25, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 19, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52]) total number of confs: 103 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517800 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517800 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517800/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517800 Building REAL300004517801 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517801' /scratch/stefan/7774842/working/building/REAL300004517801 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517801 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517801/0 /scratch/stefan/7774842/working/building/REAL300004517801 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 843) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/843 `/scratch/stefan/7774842/working/3D/843' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC=C(C(=O)[O-])N1C) `REAL300004517801.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517801.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517801/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517801 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC=C(C(=O)[O-])N1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 11, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [26, 23, 23, 22, 23, 25, 23, 11, 8, 11, 14, 14, 14, 1, 8, 1, 1, 1, 1, 1, 2, 2, 1, 1, 26, 26, 26, 26, 26, 25, 25, 25, 25, 25, 23, 23, 23, 23, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 2, 2, 2] 28 rigid atoms, others: [48, 13, 47, 16, 17, 18, 19, 22, 23, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 49, 50, 51]) total number of confs: 142 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517801 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517801 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517801/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517801 Building REAL300004517802 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517802' /scratch/stefan/7774842/working/building/REAL300004517802 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517802 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517802/0 /scratch/stefan/7774842/working/building/REAL300004517802 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 844) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/844 `/scratch/stefan/7774842/working/3D/844' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC=C(CCC(=O)[O-])C=C1) `REAL300004517802.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517802.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517802/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517802 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC=C(CCC(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 5, 5, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 7 conformations in input total number of sets (complete confs): 7 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 5, 4, 4, 4, 4, 5, 5, 5, 1, 4, 1, 1, 1, 1, 1, 2, 5, 5, 5, 1, 1, 4, 4, 4, 4, 4, 5, 5, 5, 5, 5, 4, 4, 4, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 1, 1, 2, 2, 5, 5, 1, 1] 7 rigid atoms, others: [50, 17, 13, 15, 16, 49, 18, 19, 56, 55, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 51, 52, 53, 54]) total number of confs: 42 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517802 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517802 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517802/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517802 Building REAL300004517803 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517803' /scratch/stefan/7774842/working/building/REAL300004517803 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517803 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517803/0 /scratch/stefan/7774842/working/building/REAL300004517803 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 845) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/845 `/scratch/stefan/7774842/working/3D/845' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)CC1(CC(=O)[O-])CC1) `REAL300004517803.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517803.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517803/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517803 none CC[NH+](CC)CCN(CC(C)C)C(=O)CC1(CC(=O)[O-])CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 5, 5, 5, 1, 11, 11, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [16, 12, 12, 12, 12, 14, 12, 7, 6, 7, 7, 7, 7, 3, 6, 1, 1, 1, 3, 6, 6, 1, 1, 16, 16, 16, 16, 16, 14, 14, 14, 14, 14, 12, 12, 12, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 3, 3, 3, 1, 1, 1, 1] 18 rigid atoms, others: [15, 16, 17, 50, 51, 52, 21, 22, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 18, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 106 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517803 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517803 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517803/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517803 Building REAL300004517804 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517804' /scratch/stefan/7774842/working/building/REAL300004517804 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517804 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517804/0 /scratch/stefan/7774842/working/building/REAL300004517804 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 846) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/846 `/scratch/stefan/7774842/working/3D/846' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1CC2(C1)C(C(=O)[O-])C2(F)F) `REAL300004517804.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517804.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517804/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517804 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1CC2(C1)C(C(=O)[O-])C2(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'F', 'F', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 15, 15, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 2 conformations in input total number of sets (complete confs): 2 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1] 2 rigid atoms, others: [19, 50, 25, 17, 13, 15, 16, 49, 18, 51, 52, 53, 54, 23, 24, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 9 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517804 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517804 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517804/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517804 Building REAL300004517805 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517805' /scratch/stefan/7774842/working/building/REAL300004517805 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517805 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517805/0 /scratch/stefan/7774842/working/building/REAL300004517805 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 847) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/847 `/scratch/stefan/7774842/working/3D/847' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CSC(C(=O)[O-])=N1) `REAL300004517805.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517805/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517805 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CSC(C(=O)[O-])=N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 14, 1, 1, 11, 11, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 13 conformations in input total number of sets (complete confs): 13 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 9, 9, 9, 11, 9, 7, 4, 7, 7, 7, 7, 1, 4, 1, 1, 1, 1, 1, 2, 2, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 9, 9, 9, 9, 7, 7, 7, 7, 7, 7, 7, 7, 7, 1] 13 rigid atoms, others: [13, 46, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 57 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517805 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517805 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517805/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517805 Building REAL300004517806 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517806' /scratch/stefan/7774842/working/building/REAL300004517806 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517806 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517806/0 /scratch/stefan/7774842/working/building/REAL300004517806 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 848) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/848 `/scratch/stefan/7774842/working/3D/848' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1=C(C)SC(C(=O)[O-])=C1) `REAL300004517806.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517806 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1=C(C)SC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 5, 14, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [21, 19, 19, 19, 19, 21, 19, 10, 6, 10, 12, 12, 12, 1, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21, 19, 19, 19, 19, 12, 12, 12, 12, 12, 12, 12, 12, 12, 2, 2, 2, 1] 23 rigid atoms, others: [50, 13, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 117 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517806 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517806 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517806/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517806 Building REAL300004517807 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517807' /scratch/stefan/7774842/working/building/REAL300004517807 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517807 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517807/0 /scratch/stefan/7774842/working/building/REAL300004517807 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 849) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/849 `/scratch/stefan/7774842/working/3D/849' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC2=C(SC(C(=O)[O-])=C2)S1) `REAL300004517807.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517807/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517807 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC2=C(SC(C(=O)[O-])=C2)S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 14, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [132, 131, 91, 131, 131, 132, 69, 35, 11, 35, 51, 53, 53, 1, 11, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 132, 132, 132, 132, 132, 132, 132, 132, 132, 132, 91, 91, 69, 69, 51, 51, 53, 53, 53, 53, 53, 53, 53, 1, 1] 139 rigid atoms, others: [50, 17, 13, 15, 16, 49, 18, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 719 number of broken/clashed sets: 139 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517807 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517807 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517807/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517807 Building REAL300004517808 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517808' /scratch/stefan/7774842/working/building/REAL300004517808 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517808 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517808/0 /scratch/stefan/7774842/working/building/REAL300004517808 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 850) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/850 `/scratch/stefan/7774842/working/3D/850' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC(OC)=CC(C(=O)[O-])=C1Cl) `REAL300004517808.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517808.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517808/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517808 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC(OC)=CC(C(=O)[O-])=C1Cl NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'Cl', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 1, 12, 5, 1, 1, 1, 11, 11, 1, 16, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 66 conformations in input total number of sets (complete confs): 66 using faster count positions algorithm for large data unique positions, atoms: [65, 62, 29, 62, 62, 63, 27, 15, 6, 15, 20, 20, 20, 1, 6, 1, 1, 1, 1, 3, 1, 1, 1, 3, 3, 1, 1, 65, 65, 65, 65, 65, 63, 63, 63, 63, 63, 29, 29, 27, 27, 20, 20, 20, 20, 20, 20, 20, 20, 20, 1, 3, 3, 3, 1] 66 rigid atoms, others: [18, 22, 13, 15, 16, 17, 50, 20, 21, 54, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 19, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 51, 52, 53]) total number of confs: 321 number of broken/clashed sets: 66 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517808 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517808 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517808/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517808 Building REAL300004517809 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517809' /scratch/stefan/7774842/working/building/REAL300004517809 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517809 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517809/0 /scratch/stefan/7774842/working/building/REAL300004517809 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 851) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/851 `/scratch/stefan/7774842/working/3D/851' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC2=C(C(=O)[O-])C=CC=C2S1) `REAL300004517809.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517809.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517809/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517809 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC2=C(C(=O)[O-])C=CC=C2S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 40 conformations in input total number of sets (complete confs): 40 using default count positions algorithm for smaller data unique positions, atoms: [37, 33, 18, 33, 33, 36, 16, 13, 8, 13, 15, 15, 15, 1, 8, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 36, 36, 36, 36, 36, 18, 18, 16, 16, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 1] 40 rigid atoms, others: [51, 18, 13, 15, 16, 17, 50, 19, 52, 53, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 197 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517809 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517809 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517809/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517809 Building REAL300004517810 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517810' /scratch/stefan/7774842/working/building/REAL300004517810 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517810 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517810/0 /scratch/stefan/7774842/working/building/REAL300004517810 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 852) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/852 `/scratch/stefan/7774842/working/3D/852' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)CCC1=CC=CN=C1C(=O)[O-]) `REAL300004517810.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517810.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517810/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517810 none CC[NH+](CC)CCN(CC(C)C)C(=O)CCC1=CC=CN=C1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 5, 5, 1, 1, 1, 1, 8, 1, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 20 conformations in input total number of sets (complete confs): 20 using default count positions algorithm for smaller data unique positions, atoms: [20, 19, 14, 19, 19, 20, 14, 13, 9, 13, 13, 13, 13, 3, 9, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 14, 14, 14, 14, 13, 13, 13, 13, 13, 13, 13, 13, 13, 3, 3, 3, 3, 1, 1, 1] 20 rigid atoms, others: [54, 23, 16, 17, 18, 19, 20, 53, 22, 55, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 92 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517810 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517810 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517810/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517810 Building REAL300004517811 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517811' /scratch/stefan/7774842/working/building/REAL300004517811 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517811 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517811/0 /scratch/stefan/7774842/working/building/REAL300004517811 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 853) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/853 `/scratch/stefan/7774842/working/3D/853' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)/C=C/C1=CC=C(C(=O)[O-])C=C1) `REAL300004517811.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517811 none CC[NH+](CC)CCN(CC(C)C)C(=O)/C=C/C1=CC=C(C(=O)[O-])C=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [140, 134, 131, 133, 134, 140, 127, 58, 20, 58, 76, 76, 76, 4, 20, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 140, 140, 140, 140, 140, 140, 140, 140, 140, 140, 131, 131, 127, 127, 76, 76, 76, 76, 76, 76, 76, 76, 76, 4, 4, 1, 1, 1, 1] 140 rigid atoms, others: [51, 16, 17, 18, 19, 20, 21, 54, 24, 25, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 683 number of broken/clashed sets: 140 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517811 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517811 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517811/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517811 Building REAL300004517812 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517812' /scratch/stefan/7774842/working/building/REAL300004517812 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517812 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517812/0 /scratch/stefan/7774842/working/building/REAL300004517812 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 854) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/854 `/scratch/stefan/7774842/working/3D/854' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC2=C(N1)C(C(=O)[O-])=CS2) `REAL300004517812.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517812 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC2=C(N1)C(C(=O)[O-])=CS2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 43 conformations in input total number of sets (complete confs): 43 using default count positions algorithm for smaller data unique positions, atoms: [38, 38, 30, 38, 38, 38, 30, 20, 10, 20, 27, 27, 27, 1, 10, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 38, 38, 38, 38, 38, 38, 38, 38, 38, 38, 30, 30, 30, 30, 27, 27, 27, 27, 27, 27, 27, 27, 27, 1, 1, 1] 43 rigid atoms, others: [51, 50, 49, 13, 15, 16, 17, 18, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 198 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517812 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517812 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517812/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517812 Building REAL300004517813 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517813' /scratch/stefan/7774842/working/building/REAL300004517813 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517813 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517813/0 /scratch/stefan/7774842/working/building/REAL300004517813 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 855) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/855 `/scratch/stefan/7774842/working/3D/855' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC2=C(C=C(C(=O)[O-])S2)N1) `REAL300004517813.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517813.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517813/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517813 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC2=C(C=C(C(=O)[O-])S2)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 14, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [107, 106, 76, 106, 106, 108, 59, 31, 11, 31, 46, 46, 46, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 107, 107, 107, 107, 107, 108, 108, 108, 108, 108, 76, 76, 59, 59, 46, 46, 46, 46, 46, 46, 46, 46, 46, 1, 1, 1] 112 rigid atoms, others: [51, 50, 17, 13, 15, 16, 49, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 593 number of broken/clashed sets: 112 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517813 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517813 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517813/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517813 Building REAL300004517814 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517814' /scratch/stefan/7774842/working/building/REAL300004517814 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517814 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517814/0 /scratch/stefan/7774842/working/building/REAL300004517814 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 856) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/856 `/scratch/stefan/7774842/working/3D/856' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC2=C(N1)C(C(=O)[O-])=CO2) `REAL300004517814.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517814/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517814 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC2=C(N1)C(C(=O)[O-])=CO2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 65 conformations in input total number of sets (complete confs): 65 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 49, 60, 60, 60, 48, 29, 11, 29, 39, 39, 39, 1, 11, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 60, 60, 60, 60, 60, 60, 60, 60, 60, 60, 49, 49, 48, 48, 39, 39, 39, 39, 39, 39, 39, 39, 39, 1, 1, 1] 65 rigid atoms, others: [51, 50, 49, 13, 15, 16, 17, 18, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 302 number of broken/clashed sets: 65 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517814 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517814 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517814/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517814 Building REAL300004517815 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517815' /scratch/stefan/7774842/working/building/REAL300004517815 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517815 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517815/0 /scratch/stefan/7774842/working/building/REAL300004517815 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 857) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/857 `/scratch/stefan/7774842/working/3D/857' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC=CC(C(=O)[O-])=C1C) `REAL300004517815.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517815 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC=CC(C(=O)[O-])=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 11 conformations in input total number of sets (complete confs): 11 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 9, 9, 9, 11, 9, 6, 4, 6, 6, 6, 6, 1, 4, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 9, 9, 9, 9, 6, 6, 6, 6, 6, 6, 6, 6, 6, 1, 1, 1, 2, 2, 2] 11 rigid atoms, others: [48, 50, 49, 13, 15, 16, 17, 18, 19, 20, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 51, 52, 53]) total number of confs: 64 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517815 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517815 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517815/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517815 Building REAL300004517816 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517816' /scratch/stefan/7774842/working/building/REAL300004517816 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517816 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517816/0 /scratch/stefan/7774842/working/building/REAL300004517816 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 858) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/858 `/scratch/stefan/7774842/working/3D/858' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C=CC1=CC=C(C(=O)[O-])N=C1) `REAL300004517816.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517816.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517816/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517816 none CC[NH+](CC)CCN(CC(C)C)C(=O)C=CC1=CC=C(C(=O)[O-])N=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 179 conformations in input total number of sets (complete confs): 179 using faster count positions algorithm for large data unique positions, atoms: [177, 166, 160, 166, 166, 179, 154, 74, 33, 74, 100, 100, 100, 5, 33, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 177, 177, 177, 177, 177, 179, 179, 179, 179, 179, 160, 160, 154, 154, 100, 100, 100, 100, 100, 100, 100, 100, 100, 5, 5, 1, 1, 1] 179 rigid atoms, others: [51, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 53, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 929 number of broken/clashed sets: 179 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517816 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517816 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517816/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517816 Building REAL300004517817 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517817' /scratch/stefan/7774842/working/building/REAL300004517817 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517817 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517817/0 /scratch/stefan/7774842/working/building/REAL300004517817 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 859) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/859 `/scratch/stefan/7774842/working/3D/859' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC(C(=O)[O-])=CS1) `REAL300004517817.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517817.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517817/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517817 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC(C(=O)[O-])=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [39, 32, 32, 32, 32, 38, 32, 19, 10, 19, 21, 21, 21, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 39, 39, 39, 39, 39, 38, 38, 38, 38, 38, 32, 32, 32, 32, 21, 21, 21, 21, 21, 21, 21, 21, 21, 1, 1] 45 rigid atoms, others: [13, 46, 15, 16, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 203 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517817 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517817 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517817/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517817 Building REAL300004517818 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517818' /scratch/stefan/7774842/working/building/REAL300004517818 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517818 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517818/0 /scratch/stefan/7774842/working/building/REAL300004517818 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 860) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/860 `/scratch/stefan/7774842/working/3D/860' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)[C@@H]1[C@H]2CC[C@H](O2)[C@@H]1C(=O)[O-]) `REAL300004517818.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517818.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517818/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517818 none CC[NH+](CC)CCN(CC(C)C)C(=O)[C@@H]1[C@H]2CC[C@H](O2)[C@@H]1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 5, 7, 5, 7, 5, 5, 5, 7, 12, 5, 7, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1] 3 rigid atoms, others: [22, 55, 13, 15, 16, 17, 18, 19, 20, 53, 54, 23, 24, 52, 25, 26, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 15 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517818 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517818 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517818/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517818 Building REAL300004517819 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517819' /scratch/stefan/7774842/working/building/REAL300004517819 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517819 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517819/0 /scratch/stefan/7774842/working/building/REAL300004517819 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 861) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/861 `/scratch/stefan/7774842/working/3D/861' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC=CC2=C(C(=O)[O-])C=CC=C12) `REAL300004517819.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517819 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1=CC=CC2=C(C(=O)[O-])C=CC=C12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 47, 31, 47, 47, 48, 26, 13, 5, 13, 19, 19, 19, 1, 5, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 1, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 31, 31, 26, 26, 19, 19, 19, 19, 19, 19, 19, 19, 19, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [19, 56, 55, 13, 15, 16, 17, 18, 51, 52, 53, 54, 25, 24, 20, 26, 27, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 22, 23, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 269 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517819 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517819 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517819/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517819 Building REAL300004517820 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517820' /scratch/stefan/7774842/working/building/REAL300004517820 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517820 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517820/0 /scratch/stefan/7774842/working/building/REAL300004517820 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 862) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/862 `/scratch/stefan/7774842/working/3D/862' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)[C@@]1(C(C)C)C[C@H]1C(=O)[O-]) `REAL300004517820.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517820/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517820 none CC[NH+](CC)CCN(CC(C)C)C(=O)[C@@]1(C(C)C)C[C@H]1C(=O)[O-] NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 5, 5, 5, 5, 5, 5, 7, 1, 11, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 3 conformations in input total number of sets (complete confs): 3 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 3, 3, 1, 1, 1, 1, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1] 3 rigid atoms, others: [13, 15, 16, 19, 20, 21, 22, 55, 56] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 17, 18, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 20 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517820 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517820 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517820/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517820 Building REAL300004517821 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517821' /scratch/stefan/7774842/working/building/REAL300004517821 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517821 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517821/0 /scratch/stefan/7774842/working/building/REAL300004517821 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 863) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/863 `/scratch/stefan/7774842/working/3D/863' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)CC1=CC=C(C(=O)[O-])C=C1C) `REAL300004517821.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517821.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517821/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517821 none CC[NH+](CC)CCN(CC(C)C)C(=O)CC1=CC=C(C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 78 conformations in input total number of sets (complete confs): 78 using faster count positions algorithm for large data unique positions, atoms: [78, 78, 48, 78, 78, 78, 43, 26, 18, 26, 29, 29, 29, 6, 18, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 48, 48, 43, 43, 29, 29, 29, 29, 29, 29, 29, 29, 29, 6, 6, 1, 1, 1, 2, 2, 2] 78 rigid atoms, others: [19, 25, 15, 16, 17, 18, 51, 52, 53, 23, 24, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 54, 55, 56]) total number of confs: 397 number of broken/clashed sets: 78 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517821 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517821 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517821/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517821 Building REAL300004517822 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517822' /scratch/stefan/7774842/working/building/REAL300004517822 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517822 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517822/0 /scratch/stefan/7774842/working/building/REAL300004517822 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 864) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/864 `/scratch/stefan/7774842/working/3D/864' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)CC1=CC(C(=O)[O-])=CS1) `REAL300004517822.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517822.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517822/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517822 none CC[NH+](CC)CCN(CC(C)C)C(=O)CC1=CC(C(=O)[O-])=CS1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 5, 1, 1, 1, 1, 11, 11, 1, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [41, 41, 29, 41, 41, 41, 28, 17, 15, 17, 17, 17, 17, 7, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 41, 41, 41, 41, 41, 41, 41, 41, 29, 29, 28, 28, 17, 17, 17, 17, 17, 17, 17, 17, 17, 7, 7, 1, 1] 41 rigid atoms, others: [49, 50, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 188 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517822 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517822 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517822/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517822 Building REAL300004517823 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517823' /scratch/stefan/7774842/working/building/REAL300004517823 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517823 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517823/0 /scratch/stefan/7774842/working/building/REAL300004517823 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 865) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/865 `/scratch/stefan/7774842/working/3D/865' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)CC1=CC=C(C(=O)[O-])C(F)=C1) `REAL300004517823.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517823 none CC[NH+](CC)CCN(CC(C)C)C(=O)CC1=CC=C(C(=O)[O-])C(F)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 5, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 80 conformations in input total number of sets (complete confs): 80 using faster count positions algorithm for large data unique positions, atoms: [79, 77, 45, 77, 77, 78, 37, 25, 18, 24, 27, 28, 28, 6, 18, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 79, 79, 79, 79, 79, 78, 78, 78, 78, 78, 45, 45, 37, 37, 27, 27, 28, 28, 28, 28, 28, 28, 28, 6, 6, 1, 1, 1] 80 rigid atoms, others: [19, 15, 16, 17, 18, 51, 52, 53, 23, 24, 25, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 410 number of broken/clashed sets: 80 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517823 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517823 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517823/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517823 Building REAL300004517824 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517824' /scratch/stefan/7774842/working/building/REAL300004517824 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517824 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517824/0 /scratch/stefan/7774842/working/building/REAL300004517824 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 866) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/866 `/scratch/stefan/7774842/working/3D/866' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)[C@H]1[C@@H](C(=O)[O-])C1(C)C) `REAL300004517824.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517824 none CC[NH+](CC)CCN(CC(C)C)C(=O)[C@H]1[C@@H](C(=O)[O-])C1(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 5, 7, 5, 7, 1, 11, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2] 3 rigid atoms, others: [13, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 27 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517824 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517824 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517824/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517824 Building REAL300004517825 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517825' /scratch/stefan/7774842/working/building/REAL300004517825 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517825 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517825/0 /scratch/stefan/7774842/working/building/REAL300004517825 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 867) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/867 `/scratch/stefan/7774842/working/3D/867' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[NH+](CC)CCN(CC(C)C)C(=O)C1=C2CCCCC2=C(C(=O)[O-])S1) `REAL300004517825.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517825 none CC[NH+](CC)CCN(CC(C)C)C(=O)C1=C2CCCCC2=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 9, 6, 5, 5, 5, 5, 8, 5, 5, 5, 5, 1, 11, 1, 1, 5, 5, 5, 5, 1, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 15 conformations in input total number of sets (complete confs): 15 using default count positions algorithm for smaller data unique positions, atoms: [15, 15, 11, 15, 15, 15, 10, 9, 7, 9, 9, 9, 9, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 11, 11, 10, 10, 9, 9, 9, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1] 15 rigid atoms, others: [19, 50, 22, 57, 23, 13, 15, 16, 17, 18, 51, 52, 21, 54, 55, 56, 20, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 63 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517825 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517825 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517825/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517825 Building REAL300004517826 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517826' /scratch/stefan/7774842/working/building/REAL300004517826 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517826 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517826/0 /scratch/stefan/7774842/working/building/REAL300004517826 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 868) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/868 `/scratch/stefan/7774842/working/3D/868' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(C(=O)[O-])C=C2)C=C1C) `REAL300004517826.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517826 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(C(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 111, 111, 27, 5, 1, 1, 1, 1, 1, 1, 27, 87, 87, 100, 100, 95, 100, 100, 100, 100, 100, 111, 111, 111, 111, 110, 110, 111, 111, 5, 5, 1, 1, 1, 100, 100, 100, 100, 111, 111, 111, 111] 201 rigid atoms, others: [33, 34, 35, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 857 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517826 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(C(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 49, 111, 111, 111, 111, 11, 41, 41, 54, 54, 44, 54, 54, 54, 54, 54, 1, 1, 1, 2, 2, 2, 1, 1, 49, 49, 111, 111, 111, 54, 54, 54, 54, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 40, 23, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43]) total number of confs: 436 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517826 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(C(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 54, 54, 15, 6, 15, 51, 100, 100, 100, 100, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 54, 54, 54, 54, 54, 54, 54, 54, 51, 51, 100, 100, 100, 1, 1, 1, 1, 54, 54, 54, 54] 201 rigid atoms, others: [36, 37, 38, 39, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43]) total number of confs: 547 number of broken/clashed sets: 9 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517826 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517826 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517826/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517826 Building REAL300004517827 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517827' /scratch/stefan/7774842/working/building/REAL300004517827 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517827 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517827/0 /scratch/stefan/7774842/working/building/REAL300004517827 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 869) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/869 `/scratch/stefan/7774842/working/3D/869' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=CC(OCC(=O)[O-])=C2)C=C1C) `REAL300004517827.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517827.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517827/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517827 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=CC(OCC(=O)[O-])=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [49, 33, 49, 49, 18, 4, 1, 1, 1, 1, 1, 1, 18, 29, 29, 50, 50, 50, 50, 50, 98, 122, 129, 129, 50, 49, 49, 49, 49, 49, 49, 49, 49, 4, 4, 1, 1, 1, 50, 50, 50, 122, 122, 50, 49, 49, 49, 49] 201 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 456 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517827 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=CC(OCC(=O)[O-])=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 31, 49, 49, 49, 49, 11, 16, 16, 34, 34, 34, 34, 34, 90, 122, 143, 143, 34, 1, 1, 1, 2, 2, 2, 1, 1, 31, 31, 49, 49, 49, 34, 34, 34, 122, 122, 34, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 44, 25, 26, 27, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47]) total number of confs: 558 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517827 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=CC(OCC(=O)[O-])=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [34, 34, 34, 34, 18, 7, 18, 42, 50, 50, 50, 50, 1, 7, 1, 1, 1, 1, 1, 1, 7, 18, 29, 29, 1, 34, 34, 34, 34, 34, 34, 34, 34, 42, 42, 50, 50, 50, 1, 1, 1, 18, 18, 1, 34, 34, 34, 34] 201 rigid atoms, others: [38, 39, 40, 43, 12, 14, 15, 16, 17, 18, 19, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 44, 45, 46, 47]) total number of confs: 296 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517827 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517827 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517827/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517827 Building REAL300004517828 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517828' /scratch/stefan/7774842/working/building/REAL300004517828 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517828 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517828/0 /scratch/stefan/7774842/working/building/REAL300004517828 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 870) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/870 `/scratch/stefan/7774842/working/3D/870' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=CC(C(=O)[O-])=C2)C=C1C) `REAL300004517828.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517828/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517828 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=CC(C(=O)[O-])=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [54, 47, 97, 97, 23, 5, 1, 1, 1, 1, 1, 1, 23, 47, 47, 107, 107, 107, 107, 107, 107, 107, 107, 97, 97, 97, 97, 97, 97, 97, 97, 5, 5, 1, 1, 1, 107, 107, 107, 107, 97, 97, 97, 97] 201 rigid atoms, others: [33, 34, 35, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 643 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517828 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=CC(C(=O)[O-])=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 45, 97, 97, 97, 97, 11, 25, 25, 70, 70, 70, 70, 70, 70, 70, 70, 1, 1, 1, 2, 2, 2, 1, 1, 45, 45, 97, 97, 97, 70, 70, 70, 70, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 40, 23, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43]) total number of confs: 364 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517828 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=CC(C(=O)[O-])=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [49, 49, 70, 70, 25, 11, 25, 68, 107, 107, 107, 107, 1, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 70, 70, 70, 70, 70, 70, 70, 70, 68, 68, 107, 107, 107, 1, 1, 1, 1, 70, 70, 70, 70] 201 rigid atoms, others: [36, 37, 38, 39, 12, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43]) total number of confs: 577 number of broken/clashed sets: 5 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517828 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517828 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517828/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517828 Building REAL300004517829 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517829' /scratch/stefan/7774842/working/building/REAL300004517829 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517829 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517829/0 /scratch/stefan/7774842/working/building/REAL300004517829 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 871) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/871 `/scratch/stefan/7774842/working/3D/871' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(C(=O)[O-])S2)C=C1C) `REAL300004517829.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517829.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517829/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517829 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(C(=O)[O-])S2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 11, 11, 14, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [84, 59, 84, 84, 25, 5, 1, 1, 1, 1, 1, 1, 25, 55, 55, 110, 110, 110, 110, 110, 110, 110, 84, 84, 84, 84, 84, 84, 84, 84, 5, 5, 1, 1, 1, 110, 110, 84, 84, 84, 84] 201 rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40]) total number of confs: 442 number of broken/clashed sets: 2 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517829 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(C(=O)[O-])S2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 11, 11, 14, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 38, 84, 84, 84, 84, 11, 27, 27, 69, 69, 69, 69, 69, 69, 69, 1, 1, 1, 2, 2, 2, 1, 1, 38, 38, 84, 84, 84, 69, 69, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 22, 23, 24, 28, 29, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40]) total number of confs: 326 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517829 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(C(=O)[O-])S2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 11, 11, 14, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [69, 61, 69, 69, 29, 11, 29, 76, 110, 110, 110, 110, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 69, 69, 69, 69, 69, 69, 69, 69, 76, 76, 110, 110, 110, 1, 1, 69, 69, 69, 69] 201 rigid atoms, others: [35, 36, 12, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40]) total number of confs: 463 number of broken/clashed sets: 2 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517829 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517829 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517829/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517829 Building REAL300004517830 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517830' /scratch/stefan/7774842/working/building/REAL300004517830 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517830 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517830/0 /scratch/stefan/7774842/working/building/REAL300004517830 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 872) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/872 `/scratch/stefan/7774842/working/3D/872' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=CC(C(=O)[O-])=N2)C=C1C) `REAL300004517830.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517830.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517830/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517830 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=CC(C(=O)[O-])=N2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 122, 122, 23, 5, 1, 1, 1, 1, 1, 1, 23, 66, 66, 104, 104, 104, 104, 104, 104, 104, 104, 122, 122, 122, 122, 122, 122, 122, 122, 5, 5, 1, 1, 1, 104, 104, 104, 122, 122, 122, 122] 201 rigid atoms, others: [33, 34, 35, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 878 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517830 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=CC(C(=O)[O-])=N2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 56, 122, 122, 122, 122, 11, 35, 35, 93, 93, 93, 93, 93, 93, 93, 93, 1, 1, 1, 2, 2, 2, 1, 1, 56, 56, 122, 122, 122, 93, 93, 93, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 39, 23, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42]) total number of confs: 454 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517830 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=CC(C(=O)[O-])=N2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 93, 93, 29, 10, 29, 69, 104, 104, 104, 104, 1, 10, 1, 1, 1, 1, 1, 1, 2, 2, 1, 93, 93, 93, 93, 93, 93, 93, 93, 69, 69, 104, 104, 104, 1, 1, 1, 93, 93, 93, 93] 201 rigid atoms, others: [36, 37, 38, 12, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42]) total number of confs: 798 number of broken/clashed sets: 14 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517830 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517830 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517830/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517830 Building REAL300004517831 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517831' /scratch/stefan/7774842/working/building/REAL300004517831 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517831 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517831/0 /scratch/stefan/7774842/working/building/REAL300004517831 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 873) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/873 `/scratch/stefan/7774842/working/3D/873' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)CCC2=CC=C(C(=O)[O-])C=C2)C=C1C) `REAL300004517831.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517831.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517831/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517831 none CC1=CC=C(N(CC2=CC=CO2)C(=O)CCC2=CC=C(C(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [44, 35, 82, 82, 21, 5, 1, 1, 1, 1, 1, 1, 21, 44, 44, 103, 109, 109, 109, 109, 109, 109, 109, 109, 109, 82, 82, 82, 81, 82, 82, 82, 82, 5, 5, 1, 1, 1, 103, 103, 109, 109, 109, 109, 109, 109, 82, 82, 82, 82] 201 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 747 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517831 none CC1=CC=C(N(CC2=CC=CO2)C(=O)CCC2=CC=C(C(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 41, 82, 82, 82, 82, 11, 23, 23, 67, 81, 83, 83, 81, 81, 83, 83, 83, 83, 1, 1, 1, 2, 2, 2, 1, 1, 41, 41, 82, 82, 82, 67, 67, 81, 81, 83, 83, 83, 83, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 46, 25, 26, 27, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49]) total number of confs: 544 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517831 none CC1=CC=C(N(CC2=CC=CO2)C(=O)CCC2=CC=C(C(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [61, 58, 83, 83, 31, 13, 31, 86, 109, 109, 109, 109, 5, 13, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 83, 83, 83, 83, 83, 83, 83, 83, 86, 86, 109, 109, 109, 5, 5, 3, 3, 1, 1, 1, 1, 83, 83, 83, 83] 201 rigid atoms, others: [42, 43, 44, 45, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48, 49]) total number of confs: 655 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517831 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517831 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517831/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517831 Building REAL300004517832 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517832' /scratch/stefan/7774842/working/building/REAL300004517832 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517832 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517832/0 /scratch/stefan/7774842/working/building/REAL300004517832 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 874) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/874 `/scratch/stefan/7774842/working/3D/874' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=NC(C(=O)[O-])=C2)C=C1C) `REAL300004517832.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517832/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517832 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=NC(C(=O)[O-])=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 8, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [97, 51, 97, 97, 23, 5, 1, 1, 1, 1, 1, 1, 23, 42, 42, 104, 104, 104, 104, 104, 104, 104, 104, 97, 97, 97, 97, 97, 97, 97, 97, 5, 5, 1, 1, 1, 104, 104, 104, 97, 97, 97, 97] 201 rigid atoms, others: [33, 34, 35, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 482 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517832 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=NC(C(=O)[O-])=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 8, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 45, 97, 97, 97, 97, 11, 23, 23, 69, 69, 69, 69, 69, 69, 69, 69, 1, 1, 1, 2, 2, 2, 1, 1, 45, 45, 97, 97, 97, 69, 69, 69, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 39, 23, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42]) total number of confs: 355 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517832 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=NC(C(=O)[O-])=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 8, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [69, 49, 69, 69, 25, 11, 25, 71, 104, 104, 104, 104, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 69, 69, 69, 69, 69, 69, 69, 69, 71, 71, 104, 104, 104, 1, 1, 1, 69, 69, 69, 69] 201 rigid atoms, others: [36, 37, 38, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42]) total number of confs: 494 number of broken/clashed sets: 5 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517832 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517832 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517832/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517832 Building REAL300004517833 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517833' /scratch/stefan/7774842/working/building/REAL300004517833 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517833 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517833/0 /scratch/stefan/7774842/working/building/REAL300004517833 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 875) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/875 `/scratch/stefan/7774842/working/3D/875' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)C=CC2=CC=C(C(=O)[O-])C=C2)C=C1C) `REAL300004517833.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517833.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517833/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517833 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C=CC2=CC=C(C(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 45, 73, 73, 19, 5, 1, 1, 1, 1, 1, 1, 19, 42, 42, 102, 102, 115, 115, 102, 110, 115, 115, 115, 115, 73, 73, 73, 73, 73, 73, 73, 73, 5, 5, 1, 1, 1, 109, 109, 115, 115, 115, 115, 73, 73, 73, 73] 201 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 599 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517833 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C=CC2=CC=C(C(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 37, 73, 73, 73, 73, 11, 27, 27, 83, 83, 105, 105, 88, 105, 105, 105, 105, 105, 1, 1, 1, 2, 2, 2, 1, 1, 37, 37, 73, 73, 73, 83, 83, 105, 105, 105, 105, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 44, 25, 26, 27, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47]) total number of confs: 527 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517833 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C=CC2=CC=C(C(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [105, 80, 105, 105, 43, 17, 43, 92, 115, 115, 115, 115, 3, 17, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 105, 105, 105, 105, 105, 105, 105, 105, 92, 92, 115, 115, 115, 3, 3, 1, 1, 1, 1, 105, 105, 105, 105] 201 rigid atoms, others: [40, 41, 42, 43, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47]) total number of confs: 600 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517833 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517833 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517833/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517833 Building REAL300004517834 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517834' /scratch/stefan/7774842/working/building/REAL300004517834 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517834 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517834/0 /scratch/stefan/7774842/working/building/REAL300004517834 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 876) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/876 `/scratch/stefan/7774842/working/3D/876' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC(C(=O)[O-])=CC([N+](=O)[O-])=C2)C=C1C) `REAL300004517834.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517834/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517834 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC(C(=O)[O-])=CC([N+](=O)[O-])=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 23, 86, 86, 23, 4, 1, 1, 1, 1, 1, 1, 23, 48, 48, 111, 111, 111, 111, 111, 111, 111, 111, 111, 111, 111, 86, 86, 86, 84, 86, 86, 86, 86, 4, 4, 1, 1, 1, 111, 111, 111, 86, 86, 86, 86] 201 rigid atoms, others: [36, 37, 6, 7, 8, 9, 10, 11, 38] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 655 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517834 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC(C(=O)[O-])=CC([N+](=O)[O-])=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 46, 86, 86, 86, 86, 11, 27, 27, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 1, 1, 1, 2, 2, 2, 1, 1, 46, 46, 86, 86, 86, 78, 78, 78, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 42, 26, 27, 28, 5] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45]) total number of confs: 369 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517834 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC(C(=O)[O-])=CC([N+](=O)[O-])=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 27, 78, 78, 27, 11, 27, 80, 111, 111, 111, 111, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 78, 78, 78, 78, 78, 78, 78, 78, 80, 80, 111, 111, 111, 1, 1, 1, 78, 78, 78, 78] 201 rigid atoms, others: [39, 40, 41, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44, 45]) total number of confs: 728 number of broken/clashed sets: 7 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517834 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517834 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517834/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517834 Building REAL300004517835 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517835' /scratch/stefan/7774842/working/building/REAL300004517835 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517835 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517835/0 /scratch/stefan/7774842/working/building/REAL300004517835 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 877) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/877 `/scratch/stefan/7774842/working/3D/877' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC(C(=O)[O-])=CC([N+](=O)[O-])=C2)C=C1C) `REAL300004517835.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517835 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC(C(=O)[O-])=CC([N+](=O)[O-])=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [41, 23, 86, 86, 23, 4, 1, 1, 1, 1, 1, 1, 23, 48, 48, 111, 111, 111, 111, 111, 111, 111, 111, 111, 111, 111, 86, 86, 86, 84, 86, 86, 86, 86, 4, 4, 1, 1, 1, 111, 111, 111, 86, 86, 86, 86] 201 rigid atoms, others: [36, 37, 6, 7, 8, 9, 10, 11, 38] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 655 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517835 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC(C(=O)[O-])=CC([N+](=O)[O-])=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 46, 86, 86, 86, 86, 11, 27, 27, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 1, 1, 1, 2, 2, 2, 1, 1, 46, 46, 86, 86, 86, 78, 78, 78, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 42, 26, 27, 28, 5] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45]) total number of confs: 369 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517835 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC(C(=O)[O-])=CC([N+](=O)[O-])=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [53, 27, 78, 78, 27, 11, 27, 80, 111, 111, 111, 111, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 78, 78, 78, 78, 78, 78, 78, 78, 80, 80, 111, 111, 111, 1, 1, 1, 78, 78, 78, 78] 201 rigid atoms, others: [39, 40, 41, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44, 45]) total number of confs: 728 number of broken/clashed sets: 7 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517835 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517835 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517835/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517835 Building REAL300004517836 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517836' /scratch/stefan/7774842/working/building/REAL300004517836 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517836 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517836/0 /scratch/stefan/7774842/working/building/REAL300004517836 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 878) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/878 `/scratch/stefan/7774842/working/3D/878' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(C(=O)[O-])O2)C=C1C) `REAL300004517836.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517836.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517836/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517836 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(C(=O)[O-])O2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [63, 24, 95, 95, 24, 5, 1, 1, 1, 1, 1, 1, 24, 73, 73, 103, 103, 103, 103, 103, 103, 103, 95, 95, 95, 95, 95, 95, 95, 95, 5, 5, 1, 1, 1, 103, 103, 95, 95, 95, 95] 201 rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40]) total number of confs: 708 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517836 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(C(=O)[O-])O2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 46, 95, 95, 95, 95, 11, 34, 34, 82, 82, 82, 82, 82, 82, 82, 1, 1, 1, 2, 2, 2, 1, 1, 46, 46, 95, 95, 95, 82, 82, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 22, 23, 24, 28, 29, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40]) total number of confs: 394 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517836 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(C(=O)[O-])O2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [63, 29, 82, 82, 29, 10, 29, 66, 103, 103, 103, 103, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 82, 82, 82, 82, 82, 82, 82, 82, 66, 66, 103, 103, 103, 1, 1, 82, 82, 82, 82] 201 rigid atoms, others: [35, 36, 12, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40]) total number of confs: 635 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517836 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517836 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517836/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517836 Building REAL300004517837 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517837' /scratch/stefan/7774842/working/building/REAL300004517837 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517837 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517837/0 /scratch/stefan/7774842/working/building/REAL300004517837 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 879) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/879 `/scratch/stefan/7774842/working/3D/879' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)CCC2=CC=CC=C2C(=O)[O-])C=C1C) `REAL300004517837.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517837/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517837 none CC1=CC=C(N(CC2=CC=CO2)C(=O)CCC2=CC=CC=C2C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [17, 11, 27, 27, 11, 3, 1, 1, 1, 1, 1, 1, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 27, 27, 27, 27, 27, 27, 27, 27, 3, 3, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 17, 27, 27, 27, 27] 27 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 178 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517837 none CC1=CC=C(N(CC2=CC=CO2)C(=O)CCC2=CC=CC=C2C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 19, 27, 27, 27, 27, 9, 9, 9, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 2, 2, 2, 1, 1, 19, 19, 27, 27, 27, 11, 11, 11, 11, 11, 11, 11, 11, 1, 2, 2, 2] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 46, 25, 26, 27, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49]) total number of confs: 107 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517837 none CC1=CC=C(N(CC2=CC=CO2)C(=O)CCC2=CC=CC=C2C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 11, 11, 5, 3, 5, 9, 17, 17, 17, 17, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 9, 9, 17, 17, 17, 3, 3, 3, 3, 1, 1, 1, 1, 11, 11, 11, 11] 27 rigid atoms, others: [42, 43, 44, 45, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 46, 47, 48, 49]) total number of confs: 104 number of broken/clashed sets: 11 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517837 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517837 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517837/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517837 Building REAL300004517838 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517838' /scratch/stefan/7774842/working/building/REAL300004517838 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517838 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517838/0 /scratch/stefan/7774842/working/building/REAL300004517838 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 880) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/880 `/scratch/stefan/7774842/working/3D/880' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)CC2=CC=CC(C(=O)[O-])=C2)C=C1C) `REAL300004517838.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517838.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517838/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517838 none CC1=CC=C(N(CC2=CC=CO2)C(=O)CC2=CC=CC(C(=O)[O-])=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [55, 55, 55, 55, 17, 4, 1, 1, 1, 1, 1, 1, 17, 31, 31, 74, 109, 109, 109, 109, 109, 109, 109, 109, 55, 55, 55, 55, 55, 55, 55, 55, 4, 4, 1, 1, 1, 74, 74, 109, 109, 109, 109, 55, 55, 55, 55] 201 rigid atoms, others: [34, 35, 36, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 390 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517838 none CC1=CC=C(N(CC2=CC=CO2)C(=O)CC2=CC=CC(C(=O)[O-])=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 43, 55, 55, 55, 55, 11, 23, 23, 51, 100, 100, 100, 100, 100, 100, 100, 100, 1, 1, 1, 2, 2, 2, 1, 1, 43, 43, 55, 55, 55, 51, 51, 100, 100, 100, 100, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 43, 24, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46]) total number of confs: 410 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517838 none CC1=CC=C(N(CC2=CC=CO2)C(=O)CC2=CC=CC(C(=O)[O-])=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [100, 100, 100, 100, 44, 29, 44, 93, 109, 109, 109, 109, 7, 29, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 100, 100, 100, 100, 100, 100, 100, 100, 93, 93, 109, 109, 109, 7, 7, 1, 1, 1, 1, 100, 100, 100, 100] 201 rigid atoms, others: [39, 40, 41, 42, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46]) total number of confs: 497 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517838 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517838 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517838/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517838 Building REAL300004517839 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517839' /scratch/stefan/7774842/working/building/REAL300004517839 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517839 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517839/0 /scratch/stefan/7774842/working/building/REAL300004517839 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 881) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/881 `/scratch/stefan/7774842/working/3D/881' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)C2CCCC(C(=O)[O-])C2)C=C1C) `REAL300004517839.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517839.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517839/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517839 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2CCCC(C(=O)[O-])C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [30, 14, 39, 39, 14, 4, 1, 1, 1, 1, 1, 1, 14, 20, 20, 20, 20, 20, 20, 20, 22, 22, 20, 39, 39, 39, 39, 39, 39, 39, 39, 4, 4, 1, 1, 1, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20, 39, 39, 39, 39] 41 rigid atoms, others: [33, 34, 35, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 235 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517839 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2CCCC(C(=O)[O-])C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 23, 39, 39, 39, 39, 7, 11, 11, 11, 11, 11, 11, 11, 16, 16, 11, 1, 1, 1, 2, 2, 2, 1, 1, 23, 23, 39, 39, 39, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 2, 2, 2] 41 rigid atoms, others: [0, 1, 2, 3, 4, 5, 46, 23, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49]) total number of confs: 157 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517839 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2CCCC(C(=O)[O-])C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 41 conformations in input total number of sets (complete confs): 41 using default count positions algorithm for smaller data unique positions, atoms: [9, 5, 11, 11, 5, 3, 5, 12, 20, 20, 20, 20, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 1, 11, 11, 11, 11, 11, 11, 11, 11, 12, 12, 20, 20, 20, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11] 41 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 22, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 46, 47, 48, 49]) total number of confs: 107 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517839 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517839 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517839/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517839 Building REAL300004517840 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517840' /scratch/stefan/7774842/working/building/REAL300004517840 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517840 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517840/0 /scratch/stefan/7774842/working/building/REAL300004517840 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 882) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/882 `/scratch/stefan/7774842/working/3D/882' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(C(=O)[O-])N=C2)C=C1C) `REAL300004517840.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517840.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517840/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517840 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(C(=O)[O-])N=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 51, 82, 82, 25, 5, 1, 1, 1, 1, 1, 1, 25, 49, 49, 112, 112, 112, 112, 112, 112, 112, 112, 82, 82, 82, 82, 82, 82, 82, 82, 5, 5, 1, 1, 1, 112, 112, 112, 82, 82, 82, 82] 201 rigid atoms, others: [33, 34, 35, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 525 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517840 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(C(=O)[O-])N=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 37, 82, 82, 82, 82, 11, 29, 29, 65, 65, 65, 65, 65, 65, 65, 65, 1, 1, 1, 2, 2, 2, 1, 1, 37, 37, 82, 82, 82, 65, 65, 65, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 39, 23, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42]) total number of confs: 335 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517840 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(C(=O)[O-])N=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [55, 49, 65, 65, 27, 11, 27, 66, 112, 112, 112, 112, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 65, 65, 65, 65, 65, 65, 65, 65, 66, 66, 112, 112, 112, 1, 1, 1, 65, 65, 65, 65] 201 rigid atoms, others: [36, 37, 38, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42]) total number of confs: 476 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517840 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517840 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517840/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517840 Building REAL300004517841 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517841' /scratch/stefan/7774842/working/building/REAL300004517841 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517841 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517841/0 /scratch/stefan/7774842/working/building/REAL300004517841 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 883) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/883 `/scratch/stefan/7774842/working/3D/883' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(C(=O)[O-])C=N2)C=C1C) `REAL300004517841.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517841.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517841/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517841 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(C(=O)[O-])C=N2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [96, 67, 96, 96, 25, 5, 1, 1, 1, 1, 1, 1, 25, 71, 71, 97, 97, 97, 97, 97, 97, 97, 97, 96, 96, 96, 96, 96, 96, 96, 96, 5, 5, 1, 1, 1, 97, 97, 97, 96, 96, 96, 96] 201 rigid atoms, others: [33, 34, 35, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 469 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517841 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(C(=O)[O-])C=N2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 46, 96, 96, 96, 96, 11, 31, 31, 73, 73, 73, 73, 73, 73, 73, 73, 1, 1, 1, 2, 2, 2, 1, 1, 46, 46, 96, 96, 96, 73, 73, 73, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 39, 23, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42]) total number of confs: 376 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517841 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(C(=O)[O-])C=N2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 57, 73, 73, 23, 9, 23, 59, 97, 97, 97, 97, 1, 9, 1, 1, 1, 1, 1, 2, 2, 1, 1, 73, 73, 73, 73, 73, 73, 73, 73, 59, 59, 97, 97, 97, 1, 1, 1, 73, 73, 73, 73] 201 rigid atoms, others: [36, 37, 38, 12, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42]) total number of confs: 443 number of broken/clashed sets: 6 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517841 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517841 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517841/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517841 Building REAL300004517842 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517842' /scratch/stefan/7774842/working/building/REAL300004517842 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517842 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517842/0 /scratch/stefan/7774842/working/building/REAL300004517842 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 884) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/884 `/scratch/stefan/7774842/working/3D/884' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)CC(C)(C)CC(=O)[O-])C=C1C) `REAL300004517842.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517842.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517842/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517842 none CC1=CC=C(N(CC2=CC=CO2)C(=O)CC(C)(C)CC(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 65, 65, 19, 5, 1, 1, 1, 1, 1, 1, 19, 35, 35, 51, 85, 85, 85, 120, 122, 122, 65, 65, 65, 65, 64, 64, 65, 65, 5, 5, 1, 1, 1, 51, 51, 85, 85, 85, 85, 85, 85, 120, 120, 65, 65, 65, 65] 201 rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 851 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517842 none CC1=CC=C(N(CC2=CC=CO2)C(=O)CC(C)(C)CC(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 39, 65, 65, 65, 65, 11, 19, 19, 29, 74, 74, 74, 126, 130, 130, 1, 1, 1, 2, 2, 2, 1, 1, 39, 39, 65, 65, 65, 29, 29, 74, 74, 74, 74, 74, 74, 126, 126, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 45, 22, 23, 24, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48]) total number of confs: 702 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517842 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517842 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517842/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517842 Building REAL300004517843 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517843' /scratch/stefan/7774842/working/building/REAL300004517843 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517843 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517843/0 /scratch/stefan/7774842/working/building/REAL300004517843 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 885) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/885 `/scratch/stefan/7774842/working/3D/885' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(C(=O)[O-])C=C2F)C=C1C) `REAL300004517843.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517843 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(C(=O)[O-])C=C2F)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [96, 56, 96, 96, 25, 5, 1, 1, 1, 1, 1, 1, 25, 65, 65, 116, 116, 105, 116, 116, 116, 116, 116, 116, 96, 96, 96, 96, 96, 96, 96, 96, 5, 5, 1, 1, 1, 116, 116, 116, 96, 96, 96, 96] 201 rigid atoms, others: [34, 35, 36, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 576 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517843 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(C(=O)[O-])C=C2F)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 49, 96, 96, 96, 96, 11, 35, 35, 73, 73, 61, 73, 73, 73, 73, 73, 73, 1, 1, 1, 2, 2, 2, 1, 1, 49, 49, 96, 96, 96, 73, 73, 73, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 40, 24, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43]) total number of confs: 453 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517843 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(C(=O)[O-])C=C2F)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 61, 73, 73, 27, 7, 27, 80, 116, 116, 116, 116, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 73, 73, 73, 73, 73, 73, 73, 73, 80, 80, 116, 116, 116, 1, 1, 1, 73, 73, 73, 73] 201 rigid atoms, others: [37, 38, 39, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43]) total number of confs: 493 number of broken/clashed sets: 6 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517843 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517843 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517843/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517843 Building REAL300004517844 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517844' /scratch/stefan/7774842/working/building/REAL300004517844 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517844 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517844/0 /scratch/stefan/7774842/working/building/REAL300004517844 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 886) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/886 `/scratch/stefan/7774842/working/3D/886' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CN=C(C(=O)[O-])C=N2)C=C1C) `REAL300004517844.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517844/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517844 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CN=C(C(=O)[O-])C=N2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 8, 1, 1, 11, 11, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 3, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [97, 65, 97, 97, 23, 5, 1, 1, 1, 1, 1, 1, 23, 73, 73, 102, 102, 102, 102, 102, 102, 102, 102, 97, 97, 97, 97, 97, 97, 97, 97, 5, 5, 1, 1, 1, 102, 102, 97, 97, 97, 97] 201 rigid atoms, others: [33, 34, 35, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41]) total number of confs: 494 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517844 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CN=C(C(=O)[O-])C=N2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 8, 1, 1, 11, 11, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 3, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 47, 97, 97, 97, 97, 11, 31, 31, 74, 74, 74, 74, 74, 74, 74, 74, 1, 1, 1, 2, 2, 2, 1, 1, 47, 47, 97, 97, 97, 74, 74, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 38, 23, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41]) total number of confs: 379 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517844 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CN=C(C(=O)[O-])C=N2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 8, 1, 1, 11, 11, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 3, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [74, 58, 74, 74, 24, 10, 24, 65, 102, 102, 102, 102, 1, 10, 1, 1, 1, 1, 1, 2, 2, 1, 1, 74, 74, 74, 74, 74, 74, 74, 74, 65, 65, 102, 102, 102, 1, 1, 74, 74, 74, 74] 201 rigid atoms, others: [36, 37, 12, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41]) total number of confs: 464 number of broken/clashed sets: 5 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517844 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517844 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517844/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517844 Building REAL300004517845 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517845' /scratch/stefan/7774842/working/building/REAL300004517845 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517845 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517845/0 /scratch/stefan/7774842/working/building/REAL300004517845 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 887) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/887 `/scratch/stefan/7774842/working/3D/887' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@H]2CC[C@H](C(=O)[O-])CC2)C=C1C) `REAL300004517845.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517845.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517845/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517845 none CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@H]2CC[C@H](C(=O)[O-])CC2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 11, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [42, 23, 116, 116, 23, 5, 1, 1, 1, 1, 1, 1, 23, 65, 65, 94, 94, 94, 94, 94, 94, 106, 106, 94, 94, 116, 116, 116, 116, 116, 116, 116, 116, 5, 5, 1, 1, 1, 94, 94, 94, 94, 94, 94, 94, 94, 116, 116, 116, 116] 201 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 969 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517845 none CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@H]2CC[C@H](C(=O)[O-])CC2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 11, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 53, 116, 116, 116, 116, 11, 27, 27, 48, 48, 48, 48, 48, 48, 74, 74, 48, 48, 1, 1, 1, 2, 2, 2, 1, 1, 53, 53, 116, 116, 116, 48, 48, 48, 48, 48, 48, 48, 48, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 46, 25, 26, 27, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49]) total number of confs: 519 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517845 none CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@H]2CC[C@H](C(=O)[O-])CC2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 11, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [33, 18, 48, 48, 18, 6, 18, 49, 94, 94, 94, 94, 1, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 48, 48, 48, 48, 48, 48, 48, 48, 49, 49, 94, 94, 94, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48] 201 rigid atoms, others: [38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 20, 23, 24, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 46, 47, 48, 49]) total number of confs: 467 number of broken/clashed sets: 10 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517845 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517845 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517845/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517845 Building REAL300004517846 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517846' /scratch/stefan/7774842/working/building/REAL300004517846 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517846 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517846/0 /scratch/stefan/7774842/working/building/REAL300004517846 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 888) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/888 `/scratch/stefan/7774842/working/3D/888' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)C2CCC(C(=O)[O-])CC2)C=C1C) `REAL300004517846.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517846.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517846/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517846 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2CCC(C(=O)[O-])CC2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 5, 5, 5, 1, 11, 11, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [115, 115, 115, 115, 23, 4, 1, 1, 1, 1, 1, 1, 23, 65, 65, 93, 93, 93, 93, 103, 103, 93, 93, 115, 115, 115, 115, 115, 115, 115, 115, 4, 4, 1, 1, 1, 93, 93, 93, 93, 93, 93, 93, 93, 93, 93, 115, 115, 115, 115] 201 rigid atoms, others: [33, 34, 35, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 437 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517846 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2CCC(C(=O)[O-])CC2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 5, 5, 5, 1, 11, 11, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 53, 115, 115, 115, 115, 11, 27, 27, 47, 47, 47, 47, 73, 73, 47, 47, 1, 1, 1, 2, 2, 2, 1, 1, 53, 53, 115, 115, 115, 47, 47, 47, 47, 47, 47, 47, 47, 47, 47, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 46, 23, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49]) total number of confs: 515 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517846 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2CCC(C(=O)[O-])CC2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 5, 5, 5, 1, 11, 11, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 47, 47, 18, 6, 18, 49, 93, 93, 93, 93, 1, 6, 1, 1, 1, 1, 1, 3, 3, 1, 1, 47, 47, 47, 47, 47, 47, 47, 47, 49, 49, 93, 93, 93, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47] 201 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 21, 22, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 46, 47, 48, 49]) total number of confs: 295 number of broken/clashed sets: 11 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517846 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517846 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517846/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517846 Building REAL300004517847 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517847' /scratch/stefan/7774842/working/building/REAL300004517847 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517847 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517847/0 /scratch/stefan/7774842/working/building/REAL300004517847 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 889) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/889 `/scratch/stefan/7774842/working/3D/889' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)CC2=CC=C(C(=O)[O-])C=C2)C=C1C) `REAL300004517847.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517847 none CC1=CC=C(N(CC2=CC=CO2)C(=O)CC2=CC=C(C(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 75, 75, 18, 3, 1, 1, 1, 1, 1, 1, 18, 41, 41, 95, 111, 111, 95, 111, 111, 111, 111, 111, 75, 75, 75, 75, 74, 74, 75, 75, 3, 3, 1, 1, 1, 95, 95, 111, 111, 111, 111, 75, 75, 75, 75] 201 rigid atoms, others: [34, 35, 36, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 839 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517847 none CC1=CC=C(N(CC2=CC=CO2)C(=O)CC2=CC=C(C(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 49, 75, 75, 75, 75, 11, 27, 27, 73, 89, 89, 73, 89, 89, 89, 89, 89, 1, 1, 1, 2, 2, 2, 1, 1, 49, 49, 75, 75, 75, 73, 73, 89, 89, 89, 89, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 43, 24, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46]) total number of confs: 566 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517847 none CC1=CC=C(N(CC2=CC=CO2)C(=O)CC2=CC=C(C(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 89, 89, 37, 16, 38, 93, 111, 111, 111, 111, 4, 16, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 89, 89, 89, 89, 89, 89, 89, 89, 93, 93, 111, 111, 111, 4, 4, 1, 1, 1, 1, 89, 89, 89, 89] 201 rigid atoms, others: [39, 40, 41, 42, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46]) total number of confs: 848 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517847 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517847 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517847/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517847 Building REAL300004517848 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517848' /scratch/stefan/7774842/working/building/REAL300004517848 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517848 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517848/0 /scratch/stefan/7774842/working/building/REAL300004517848 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 890) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/890 `/scratch/stefan/7774842/working/3D/890' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)CN2C=C(C(=O)[O-])N=N2)C=C1C) `REAL300004517848.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517848.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517848/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517848 none CC1=CC=C(N(CC2=CC=CO2)C(=O)CN2C=C(C(=O)[O-])N=N2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 8, 1, 1, 1, 11, 11, 8, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 48, 48, 48, 15, 2, 1, 1, 1, 1, 1, 1, 15, 26, 26, 65, 111, 111, 111, 111, 111, 111, 111, 48, 48, 48, 48, 48, 48, 48, 48, 2, 2, 1, 1, 1, 65, 65, 111, 48, 48, 48, 48] 201 rigid atoms, others: [33, 34, 35, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 364 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517848 none CC1=CC=C(N(CC2=CC=CO2)C(=O)CN2C=C(C(=O)[O-])N=N2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 8, 1, 1, 1, 11, 11, 8, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 31, 48, 48, 48, 48, 7, 13, 13, 43, 107, 107, 107, 107, 107, 107, 107, 1, 1, 1, 2, 2, 2, 1, 1, 31, 31, 48, 48, 48, 43, 43, 107, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 39, 23, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42]) total number of confs: 378 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517848 none CC1=CC=C(N(CC2=CC=CO2)C(=O)CN2C=C(C(=O)[O-])N=N2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 8, 1, 1, 1, 11, 11, 8, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 107, 107, 107, 56, 35, 56, 107, 111, 111, 111, 111, 8, 35, 1, 1, 1, 1, 1, 2, 2, 1, 1, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107, 111, 111, 111, 8, 8, 1, 107, 107, 107, 107] 201 rigid atoms, others: [38, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 39, 40, 41, 42]) total number of confs: 518 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517848 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517848 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517848/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517848 Building REAL300004517849 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517849' /scratch/stefan/7774842/working/building/REAL300004517849 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517849 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517849/0 /scratch/stefan/7774842/working/building/REAL300004517849 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 891) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/891 `/scratch/stefan/7774842/working/3D/891' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(C(=O)[O-])C(C)=N2)C=C1C) `REAL300004517849.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517849.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517849/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517849 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(C(=O)[O-])C(C)=N2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 5, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [78, 52, 78, 78, 23, 5, 1, 1, 1, 1, 1, 1, 23, 61, 61, 81, 81, 81, 81, 101, 101, 81, 81, 81, 78, 78, 78, 78, 78, 78, 78, 78, 5, 5, 1, 1, 1, 81, 81, 81, 81, 81, 78, 78, 78, 78] 201 rigid atoms, others: [34, 35, 36, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 476 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517849 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(C(=O)[O-])C(C)=N2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 5, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 41, 78, 78, 78, 78, 11, 35, 35, 72, 72, 72, 72, 99, 99, 72, 72, 72, 1, 1, 1, 2, 2, 2, 1, 1, 41, 41, 78, 78, 78, 72, 72, 72, 72, 72, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 42, 24, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45]) total number of confs: 451 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517849 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(C(=O)[O-])C(C)=N2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 5, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [72, 52, 72, 72, 23, 10, 23, 54, 81, 81, 81, 81, 1, 10, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 72, 72, 72, 72, 72, 72, 72, 72, 54, 54, 81, 81, 81, 1, 1, 2, 2, 2, 72, 72, 72, 72] 201 rigid atoms, others: [37, 38, 12, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 438 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517849 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517849 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517849/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517849 Building REAL300004517850 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517850' /scratch/stefan/7774842/working/building/REAL300004517850 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517850 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517850/0 /scratch/stefan/7774842/working/building/REAL300004517850 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 892) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/892 `/scratch/stefan/7774842/working/3D/892' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(C(=O)[O-])C=C2)C=C1C) `REAL300004517850.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517850.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517850/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517850 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(C(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 27, 111, 111, 27, 5, 1, 1, 1, 1, 1, 1, 27, 87, 87, 100, 100, 95, 100, 100, 100, 100, 100, 111, 111, 111, 111, 110, 110, 111, 111, 5, 5, 1, 1, 1, 100, 100, 100, 100, 111, 111, 111, 111] 201 rigid atoms, others: [33, 34, 35, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 857 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517850 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(C(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 49, 111, 111, 111, 111, 11, 41, 41, 54, 54, 44, 54, 54, 54, 54, 54, 1, 1, 1, 2, 2, 2, 1, 1, 49, 49, 111, 111, 111, 54, 54, 54, 54, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 40, 23, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43]) total number of confs: 436 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517850 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(C(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 54, 54, 15, 6, 15, 51, 100, 100, 100, 100, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 54, 54, 54, 54, 54, 54, 54, 54, 51, 51, 100, 100, 100, 1, 1, 1, 1, 54, 54, 54, 54] 201 rigid atoms, others: [36, 37, 38, 39, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43]) total number of confs: 547 number of broken/clashed sets: 9 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517850 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517850 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517850/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517850 Building REAL300004517851 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517851' /scratch/stefan/7774842/working/building/REAL300004517851 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517851 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517851/0 /scratch/stefan/7774842/working/building/REAL300004517851 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 893) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/893 `/scratch/stefan/7774842/working/3D/893' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@H]2CC[C@@H](C(=O)[O-])C2)C=C1C) `REAL300004517851.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517851.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517851/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517851 none CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@H]2CC[C@@H](C(=O)[O-])C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 11, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 37, 93, 93, 23, 5, 1, 1, 1, 1, 1, 1, 23, 53, 53, 103, 103, 103, 103, 103, 103, 108, 108, 103, 93, 93, 93, 93, 93, 93, 93, 93, 5, 5, 1, 1, 1, 103, 103, 103, 103, 103, 103, 93, 93, 93, 93] 201 rigid atoms, others: [34, 35, 36, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 806 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517851 none CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@H]2CC[C@@H](C(=O)[O-])C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 11, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 42, 93, 93, 93, 93, 11, 25, 25, 48, 48, 48, 48, 48, 48, 73, 73, 48, 1, 1, 1, 2, 2, 2, 1, 1, 42, 42, 93, 93, 93, 48, 48, 48, 48, 48, 48, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 43, 24, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46]) total number of confs: 458 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517851 none CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@H]2CC[C@@H](C(=O)[O-])C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 11, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 35, 48, 48, 19, 6, 19, 59, 103, 103, 103, 103, 1, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 48, 48, 48, 48, 48, 48, 48, 48, 59, 59, 103, 103, 103, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48] 201 rigid atoms, others: [37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45, 46]) total number of confs: 528 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517851 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517851 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517851/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517851 Building REAL300004517852 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517852' /scratch/stefan/7774842/working/building/REAL300004517852 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517852 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517852/0 /scratch/stefan/7774842/working/building/REAL300004517852 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 894) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/894 `/scratch/stefan/7774842/working/3D/894' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=CC(CC(=O)[O-])=C2)C=C1C) `REAL300004517852.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517852.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517852/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517852 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=CC(CC(=O)[O-])=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 69, 69, 21, 5, 1, 1, 1, 1, 1, 1, 21, 47, 47, 87, 87, 47, 87, 87, 101, 107, 107, 87, 69, 69, 69, 69, 69, 69, 69, 69, 5, 5, 1, 1, 1, 87, 87, 47, 101, 101, 87, 69, 69, 69, 69] 201 rigid atoms, others: [34, 35, 36, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 634 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517852 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=CC(CC(=O)[O-])=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 37, 69, 69, 69, 69, 11, 35, 35, 70, 70, 35, 70, 70, 91, 111, 111, 70, 1, 1, 1, 2, 2, 2, 1, 1, 37, 37, 69, 69, 69, 70, 70, 35, 91, 91, 70, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 43, 24, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46]) total number of confs: 598 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517852 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=CC(CC(=O)[O-])=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 70, 70, 24, 8, 24, 58, 87, 87, 87, 87, 1, 8, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 70, 70, 70, 70, 70, 70, 70, 70, 58, 58, 87, 87, 87, 1, 1, 1, 2, 2, 1, 70, 70, 70, 70] 201 rigid atoms, others: [37, 38, 39, 42, 12, 14, 15, 16, 17, 18, 19, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 43, 44, 45, 46]) total number of confs: 471 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517852 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517852 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517852/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517852 Building REAL300004517853 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517853' /scratch/stefan/7774842/working/building/REAL300004517853 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517853 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517853/0 /scratch/stefan/7774842/working/building/REAL300004517853 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 895) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/895 `/scratch/stefan/7774842/working/3D/895' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=C(CC(=O)[O-])OC=C2)C=C1C) `REAL300004517853.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517853/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517853 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=C(CC(=O)[O-])OC=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 5, 1, 11, 11, 12, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 92, 92, 25, 4, 1, 1, 1, 1, 1, 1, 25, 65, 65, 99, 99, 101, 102, 102, 99, 99, 99, 92, 92, 92, 92, 92, 92, 92, 92, 4, 4, 1, 1, 1, 101, 101, 99, 99, 92, 92, 92, 92] 201 rigid atoms, others: [33, 34, 35, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 730 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517853 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=C(CC(=O)[O-])OC=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 5, 1, 11, 11, 12, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 46, 92, 92, 92, 92, 11, 37, 37, 83, 83, 87, 113, 113, 83, 83, 83, 1, 1, 1, 2, 2, 2, 1, 1, 46, 46, 92, 92, 92, 87, 87, 83, 83, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 40, 23, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43]) total number of confs: 512 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517853 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=C(CC(=O)[O-])OC=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 5, 1, 11, 11, 12, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 83, 83, 29, 9, 29, 66, 99, 99, 99, 99, 1, 9, 1, 1, 1, 2, 7, 7, 1, 1, 1, 83, 83, 83, 83, 83, 83, 83, 83, 66, 66, 99, 99, 99, 2, 2, 1, 1, 83, 83, 83, 83] 201 rigid atoms, others: [38, 39, 12, 14, 15, 16, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 17, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 743 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517853 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517853 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517853/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517853 Building REAL300004517854 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517854' /scratch/stefan/7774842/working/building/REAL300004517854 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517854 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517854/0 /scratch/stefan/7774842/working/building/REAL300004517854 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 896) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/896 `/scratch/stefan/7774842/working/3D/896' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=COC(CC(=O)[O-])=C1C(=O)N(CC1=CC=CO1)C1=CC=C(C)C(C)=C1) `REAL300004517854.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517854 none CC1=COC(CC(=O)[O-])=C1C(=O)N(CC1=CC=CO1)C1=CC=C(C)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 5, 1, 11, 11, 1, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [51, 51, 51, 51, 51, 51, 56, 56, 56, 42, 21, 42, 5, 1, 1, 1, 1, 1, 1, 21, 64, 64, 46, 64, 64, 64, 64, 51, 51, 51, 51, 56, 56, 5, 5, 1, 1, 1, 64, 64, 64, 64, 64, 64, 64, 64, 64] 112 rigid atoms, others: [35, 36, 37, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 302 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517854 none CC1=COC(CC(=O)[O-])=C1C(=O)N(CC1=CC=CO1)C1=CC=C(C)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 5, 1, 11, 11, 1, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 7, 7, 20, 34, 51, 51, 51, 51, 20, 62, 62, 50, 62, 62, 62, 62, 2, 2, 2, 1, 2, 2, 34, 34, 51, 51, 51, 62, 62, 62, 62, 62, 62, 62, 62, 62] 112 rigid atoms, others: [0, 1, 2, 3, 4, 5, 9, 10, 30] set([6, 7, 8, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 298 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517854 none CC1=COC(CC(=O)[O-])=C1C(=O)N(CC1=CC=CO1)C1=CC=C(C)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 12, 1, 5, 1, 11, 11, 1, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 112 conformations in input total number of sets (complete confs): 112 using faster count positions algorithm for large data unique positions, atoms: [62, 62, 62, 62, 62, 62, 66, 83, 83, 36, 11, 36, 1, 11, 34, 64, 64, 64, 64, 1, 1, 1, 1, 1, 1, 1, 1, 62, 62, 62, 62, 66, 66, 34, 34, 64, 64, 64, 1, 1, 2, 2, 2, 2, 2, 2, 1] 112 rigid atoms, others: [38, 39, 12, 46, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 44, 45]) total number of confs: 376 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517854 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517854 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517854/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517854 Building REAL300004517855 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517855' /scratch/stefan/7774842/working/building/REAL300004517855 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517855 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517855/0 /scratch/stefan/7774842/working/building/REAL300004517855 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 897) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/897 `/scratch/stefan/7774842/working/3D/897' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC(C(=O)[O-])=CC=N2)C=C1C) `REAL300004517855.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517855/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517855 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC(C(=O)[O-])=CC=N2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [88, 52, 88, 88, 23, 5, 1, 1, 1, 1, 1, 1, 23, 53, 53, 104, 104, 104, 104, 104, 104, 104, 104, 88, 88, 88, 88, 88, 88, 88, 88, 5, 5, 1, 1, 1, 104, 104, 104, 88, 88, 88, 88] 201 rigid atoms, others: [33, 34, 35, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 435 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517855 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC(C(=O)[O-])=CC=N2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 45, 88, 88, 88, 88, 11, 27, 27, 71, 71, 71, 71, 71, 71, 71, 71, 1, 1, 1, 2, 2, 2, 1, 1, 45, 45, 88, 88, 88, 71, 71, 71, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 39, 23, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42]) total number of confs: 351 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517855 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC(C(=O)[O-])=CC=N2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 45, 71, 71, 24, 10, 24, 68, 104, 104, 104, 104, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 71, 71, 71, 71, 71, 71, 71, 71, 68, 68, 104, 104, 104, 1, 1, 1, 71, 71, 71, 71] 201 rigid atoms, others: [36, 37, 38, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42]) total number of confs: 496 number of broken/clashed sets: 7 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517855 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517855 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517855/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517855 Building REAL300004517856 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517856' /scratch/stefan/7774842/working/building/REAL300004517856 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517856 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517856/0 /scratch/stefan/7774842/working/building/REAL300004517856 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 898) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/898 `/scratch/stefan/7774842/working/3D/898' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)CC2CCC(C(=O)[O-])CC2)C=C1C) `REAL300004517856.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517856 none CC1=CC=C(N(CC2=CC=CO2)C(=O)CC2CCC(C(=O)[O-])CC2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 15, 51, 51, 14, 3, 1, 1, 1, 1, 1, 1, 14, 25, 25, 79, 99, 99, 99, 99, 123, 123, 99, 99, 51, 51, 51, 51, 51, 51, 51, 51, 3, 3, 1, 1, 1, 79, 79, 99, 99, 99, 99, 99, 99, 99, 99, 99, 99, 51, 51, 51, 51] 201 rigid atoms, others: [34, 35, 36, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 709 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517856 none CC1=CC=C(N(CC2=CC=CO2)C(=O)CC2CCC(C(=O)[O-])CC2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 32, 51, 51, 51, 51, 11, 19, 19, 54, 87, 87, 87, 87, 120, 120, 87, 87, 1, 1, 1, 2, 2, 2, 1, 1, 32, 32, 51, 51, 51, 54, 54, 87, 87, 87, 87, 87, 87, 87, 87, 87, 87, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 49, 24, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52]) total number of confs: 574 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517856 none CC1=CC=C(N(CC2=CC=CO2)C(=O)CC2CCC(C(=O)[O-])CC2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [67, 38, 87, 87, 36, 19, 36, 82, 99, 99, 99, 99, 5, 19, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 87, 87, 87, 87, 87, 87, 87, 87, 82, 82, 99, 99, 99, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 87, 87, 87, 87] 201 rigid atoms, others: [48, 39, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 46, 22, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 49, 50, 51, 52]) total number of confs: 703 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517856 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517856 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517856/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517856 Building REAL300004517857 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517857' /scratch/stefan/7774842/working/building/REAL300004517857 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517857 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517857/0 /scratch/stefan/7774842/working/building/REAL300004517857 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 899) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/899 `/scratch/stefan/7774842/working/3D/899' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)CC(C)(C)CC(=O)[O-])C=C1C) `REAL300004517857.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517857 none CC1=CC=C(N(CC2=CC=CO2)C(=O)CC(C)(C)CC(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 19, 65, 65, 19, 5, 1, 1, 1, 1, 1, 1, 19, 35, 35, 51, 85, 85, 85, 120, 122, 122, 65, 65, 65, 65, 64, 64, 65, 65, 5, 5, 1, 1, 1, 51, 51, 85, 85, 85, 85, 85, 85, 120, 120, 65, 65, 65, 65] 201 rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 851 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517857 none CC1=CC=C(N(CC2=CC=CO2)C(=O)CC(C)(C)CC(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 39, 65, 65, 65, 65, 11, 19, 19, 29, 74, 74, 74, 126, 130, 130, 1, 1, 1, 2, 2, 2, 1, 1, 39, 39, 65, 65, 65, 29, 29, 74, 74, 74, 74, 74, 74, 126, 126, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 45, 22, 23, 24, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48]) total number of confs: 702 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517857 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517857 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517857/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517857 Building REAL300004517858 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517858' /scratch/stefan/7774842/working/building/REAL300004517858 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517858 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517858/0 /scratch/stefan/7774842/working/building/REAL300004517858 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 900) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/900 `/scratch/stefan/7774842/working/3D/900' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)CCCC(=O)[O-])C=C1C) `REAL300004517858.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517858 none CC1=CC=C(N(CC2=CC=CO2)C(=O)CCCC(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 5, 5, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 52, 52, 15, 5, 1, 1, 1, 1, 1, 1, 15, 31, 31, 89, 94, 114, 114, 114, 52, 52, 52, 52, 52, 52, 52, 52, 5, 5, 1, 1, 1, 89, 89, 94, 94, 114, 114, 52, 52, 52, 52] 201 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 743 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517858 none CC1=CC=C(N(CC2=CC=CO2)C(=O)CCCC(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 5, 5, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 31, 52, 52, 52, 52, 11, 21, 21, 77, 83, 115, 128, 128, 1, 1, 1, 2, 2, 2, 1, 1, 31, 31, 52, 52, 52, 77, 77, 83, 83, 115, 115, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 39, 20, 21, 22, 26, 27] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42]) total number of confs: 664 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517858 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517858 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517858/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517858 Building REAL300004517859 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517859' /scratch/stefan/7774842/working/building/REAL300004517859 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517859 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517859/0 /scratch/stefan/7774842/working/building/REAL300004517859 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 901) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/901 `/scratch/stefan/7774842/working/3D/901' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)CC(C)CC(=O)[O-])C=C1C) `REAL300004517859.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517859/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517859 none CC1=CC=C(N(CC2=CC=CO2)C(=O)CC(C)CC(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 5, 5, 5, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 52, 52, 17, 5, 1, 1, 1, 1, 1, 1, 17, 29, 29, 76, 89, 89, 115, 116, 116, 52, 52, 52, 52, 52, 52, 52, 52, 5, 5, 1, 1, 1, 76, 76, 89, 89, 89, 89, 115, 115, 52, 52, 52, 52] 201 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 775 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517859 none CC1=CC=C(N(CC2=CC=CO2)C(=O)CC(C)CC(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 5, 5, 5, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 38, 52, 52, 52, 52, 11, 20, 20, 66, 89, 89, 143, 152, 152, 1, 1, 1, 2, 2, 2, 1, 1, 38, 38, 52, 52, 52, 66, 66, 89, 89, 89, 89, 143, 143, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 42, 21, 22, 23, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45]) total number of confs: 810 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517859 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517859 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517859/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517859 Building REAL300004517860 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517860' /scratch/stefan/7774842/working/building/REAL300004517860 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517860 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517860/0 /scratch/stefan/7774842/working/building/REAL300004517860 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 902) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/902 `/scratch/stefan/7774842/working/3D/902' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=NC3=C(C(=O)[O-])C=NN32)C=C1C) `REAL300004517860.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517860.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517860/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517860 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=NC3=C(C(=O)[O-])C=NN32)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 8, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [100, 100, 100, 100, 22, 5, 1, 1, 1, 1, 1, 1, 22, 54, 54, 90, 90, 90, 90, 90, 90, 98, 98, 90, 90, 90, 100, 100, 100, 100, 100, 100, 100, 100, 5, 5, 1, 1, 1, 90, 90, 90, 100, 100, 100, 100] 201 rigid atoms, others: [36, 37, 6, 7, 8, 9, 10, 11, 38] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 337 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517860 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=NC3=C(C(=O)[O-])C=NN32)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 8, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 57, 100, 100, 100, 100, 11, 39, 39, 76, 76, 76, 76, 76, 76, 90, 90, 76, 76, 76, 1, 1, 1, 2, 2, 2, 1, 1, 57, 57, 100, 100, 100, 76, 76, 76, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 42, 26, 27, 28, 5] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45]) total number of confs: 468 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517860 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=NC3=C(C(=O)[O-])C=NN32)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 8, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [76, 76, 76, 76, 23, 7, 23, 64, 90, 90, 90, 90, 1, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 76, 76, 76, 76, 76, 76, 76, 76, 64, 64, 90, 90, 90, 1, 1, 1, 76, 76, 76, 76] 201 rigid atoms, others: [39, 40, 41, 12, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 21, 22, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 42, 43, 44, 45]) total number of confs: 368 number of broken/clashed sets: 5 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517860 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517860 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517860/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517860 Building REAL300004517861 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517861' /scratch/stefan/7774842/working/building/REAL300004517861 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517861 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517861/0 /scratch/stefan/7774842/working/building/REAL300004517861 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 903) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/903 `/scratch/stefan/7774842/working/3D/903' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=NOC(C(=O)[O-])=C2)C=C1C) `REAL300004517861.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517861.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517861/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517861 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=NOC(C(=O)[O-])=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 8, 12, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 23, 85, 85, 23, 5, 1, 1, 1, 1, 1, 1, 23, 58, 58, 108, 108, 108, 108, 108, 108, 108, 85, 85, 85, 85, 85, 85, 85, 85, 5, 5, 1, 1, 1, 108, 85, 85, 85, 85] 201 rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39]) total number of confs: 634 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517861 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=NOC(C(=O)[O-])=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 8, 12, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 43, 85, 85, 85, 85, 11, 27, 27, 78, 78, 78, 78, 78, 78, 78, 1, 1, 1, 2, 2, 2, 1, 1, 43, 43, 85, 85, 85, 78, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 22, 23, 24, 36, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 30, 31, 32, 33, 34, 35, 37, 38, 39]) total number of confs: 349 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517861 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=NOC(C(=O)[O-])=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 8, 12, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [68, 39, 78, 78, 36, 12, 36, 67, 108, 108, 108, 108, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 78, 78, 78, 78, 78, 78, 78, 78, 67, 67, 108, 108, 108, 1, 78, 78, 78, 78] 201 rigid atoms, others: [35, 12, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39]) total number of confs: 586 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517861 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517861 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517861/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517861 Building REAL300004517862 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517862' /scratch/stefan/7774842/working/building/REAL300004517862 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517862 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517862/0 /scratch/stefan/7774842/working/building/REAL300004517862 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 904) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/904 `/scratch/stefan/7774842/working/3D/904' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)N(CC2=CC=CO2)C2=CC=C(C)C(C)=C2)C=C(C(=O)[O-])O1) `REAL300004517862.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517862.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517862/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517862 none CC1=C(C(=O)N(CC2=CC=CO2)C2=CC=C(C)C(C)=C2)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 1, 5, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [97, 97, 60, 23, 60, 4, 1, 1, 1, 1, 1, 1, 23, 76, 76, 23, 23, 76, 76, 76, 97, 97, 97, 97, 97, 97, 97, 97, 97, 4, 4, 1, 1, 1, 76, 76, 74, 76, 76, 76, 76, 76, 76, 97] 201 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 621 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517862 none CC1=C(C(=O)N(CC2=CC=CO2)C2=CC=C(C)C(C)=C2)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 1, 5, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 9, 9, 25, 64, 97, 97, 97, 97, 25, 78, 78, 25, 25, 78, 78, 78, 1, 1, 1, 1, 1, 1, 2, 2, 2, 64, 64, 97, 97, 97, 78, 78, 78, 78, 78, 78, 78, 78, 78, 1] 201 rigid atoms, others: [0, 1, 2, 3, 43, 20, 21, 22, 23, 24, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 695 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517862 none CC1=C(C(=O)N(CC2=CC=CO2)C2=CC=C(C)C(C)=C2)C=C(C(=O)[O-])O1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 1, 5, 1, 1, 1, 1, 11, 11, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [78, 78, 28, 11, 28, 1, 11, 35, 76, 76, 76, 76, 1, 1, 1, 1, 1, 1, 1, 1, 78, 78, 78, 78, 78, 78, 78, 78, 78, 35, 35, 76, 76, 76, 1, 1, 2, 2, 2, 2, 2, 2, 1, 78] 201 rigid atoms, others: [34, 35, 5, 42, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 43]) total number of confs: 334 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517862 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517862 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517862/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517862 Building REAL300004517863 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517863' /scratch/stefan/7774842/working/building/REAL300004517863 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517863 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517863/0 /scratch/stefan/7774842/working/building/REAL300004517863 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 905) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/905 `/scratch/stefan/7774842/working/3D/905' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)[O-])OC(C(=O)N(CC2=CC=CO2)C2=CC=C(C)C(C)=C2)=C1) `REAL300004517863.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517863.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517863/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517863 none CC1=C(C(=O)[O-])OC(C(=O)N(CC2=CC=CO2)C2=CC=C(C)C(C)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 71, 71, 71, 86, 86, 71, 56, 25, 56, 5, 1, 1, 1, 1, 1, 1, 25, 96, 96, 25, 25, 96, 96, 96, 71, 71, 71, 71, 5, 5, 1, 1, 1, 96, 96, 94, 95, 95, 96, 96, 96, 96, 71] 201 rigid atoms, others: [32, 33, 11, 12, 13, 14, 15, 16, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 741 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517863 none CC1=C(C(=O)[O-])OC(C(=O)N(CC2=CC=CO2)C2=CC=C(C)C(C)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 2, 2, 1, 1, 1, 8, 8, 21, 48, 71, 71, 71, 71, 21, 82, 82, 21, 21, 82, 82, 82, 1, 2, 2, 2, 48, 48, 71, 71, 71, 82, 82, 82, 82, 82, 82, 82, 82, 82, 1] 201 rigid atoms, others: [0, 1, 2, 3, 6, 7, 8, 43, 25] set([4, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 655 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517863 none CC1=C(C(=O)[O-])OC(C(=O)N(CC2=CC=CO2)C2=CC=C(C)C(C)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 11, 12, 1, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [82, 82, 82, 82, 102, 102, 82, 39, 11, 39, 1, 11, 49, 96, 96, 96, 96, 1, 1, 1, 1, 1, 1, 1, 1, 82, 82, 82, 82, 49, 49, 96, 96, 96, 1, 1, 2, 2, 2, 2, 2, 2, 1, 82] 201 rigid atoms, others: [34, 35, 10, 17, 18, 19, 20, 21, 22, 23, 24, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 43]) total number of confs: 482 number of broken/clashed sets: 8 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517863 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517863 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517863/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517863 Building REAL300004517864 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517864' /scratch/stefan/7774842/working/building/REAL300004517864 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517864 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517864/0 /scratch/stefan/7774842/working/building/REAL300004517864 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 906) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/906 `/scratch/stefan/7774842/working/3D/906' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)CN2C=C(C(=O)[O-])C=N2)C=C1C) `REAL300004517864.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517864.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517864/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517864 none CC1=CC=C(N(CC2=CC=CO2)C(=O)CN2C=C(C(=O)[O-])C=N2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 8, 1, 1, 1, 11, 11, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [31, 20, 44, 44, 15, 3, 1, 1, 1, 1, 1, 1, 15, 23, 23, 61, 110, 110, 110, 110, 110, 110, 110, 44, 44, 44, 44, 44, 44, 44, 44, 3, 3, 1, 1, 1, 61, 61, 110, 110, 44, 44, 44, 44] 201 rigid atoms, others: [33, 34, 35, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 497 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517864 none CC1=CC=C(N(CC2=CC=CO2)C(=O)CN2C=C(C(=O)[O-])C=N2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 8, 1, 1, 1, 11, 11, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 29, 44, 44, 44, 44, 7, 15, 15, 44, 117, 117, 117, 117, 117, 117, 117, 1, 1, 1, 2, 2, 2, 1, 1, 29, 29, 44, 44, 44, 44, 44, 117, 117, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 40, 23, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43]) total number of confs: 375 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517864 none CC1=CC=C(N(CC2=CC=CO2)C(=O)CN2C=C(C(=O)[O-])C=N2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 8, 1, 1, 1, 11, 11, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [107, 86, 117, 117, 59, 37, 59, 106, 110, 110, 110, 110, 9, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 117, 117, 117, 117, 117, 117, 117, 117, 106, 106, 110, 110, 110, 9, 9, 1, 1, 117, 117, 117, 117] 201 rigid atoms, others: [38, 39, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 697 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517864 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517864 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517864/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517864 Building REAL300004517865 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517865' /scratch/stefan/7774842/working/building/REAL300004517865 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517865 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517865/0 /scratch/stefan/7774842/working/building/REAL300004517865 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 907) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/907 `/scratch/stefan/7774842/working/3D/907' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(C=CC(=O)[O-])O2)C=C1C) `REAL300004517865.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517865.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517865/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517865 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(C=CC(=O)[O-])O2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [85, 55, 85, 85, 25, 5, 1, 1, 1, 1, 1, 1, 25, 57, 57, 86, 86, 86, 86, 114, 114, 116, 116, 86, 85, 85, 85, 85, 85, 85, 85, 85, 5, 5, 1, 1, 1, 86, 86, 114, 114, 85, 85, 85, 85] 201 rigid atoms, others: [34, 35, 36, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 553 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517865 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(C=CC(=O)[O-])O2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 41, 85, 85, 85, 85, 11, 33, 33, 56, 56, 56, 56, 107, 107, 119, 119, 56, 1, 1, 1, 2, 2, 2, 1, 1, 41, 41, 85, 85, 85, 56, 56, 107, 107, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 41, 24, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44]) total number of confs: 520 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517865 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(C=CC(=O)[O-])O2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [56, 46, 56, 56, 18, 4, 18, 50, 86, 86, 86, 86, 1, 4, 1, 1, 1, 1, 1, 7, 7, 13, 13, 1, 56, 56, 56, 56, 56, 56, 56, 56, 50, 50, 86, 86, 86, 1, 1, 7, 7, 56, 56, 56, 56] 201 rigid atoms, others: [37, 38, 12, 14, 15, 16, 17, 18, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44]) total number of confs: 387 number of broken/clashed sets: 5 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517865 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517865 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517865/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517865 Building REAL300004517866 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517866' /scratch/stefan/7774842/working/building/REAL300004517866 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517866 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517866/0 /scratch/stefan/7774842/working/building/REAL300004517866 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 908) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/908 `/scratch/stefan/7774842/working/3D/908' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(OCC(=O)[O-])C=C2)C=C1C) `REAL300004517866.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517866.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517866/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517866 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(OCC(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [27, 24, 43, 43, 15, 3, 1, 1, 1, 1, 1, 1, 15, 25, 25, 31, 31, 25, 27, 90, 120, 120, 120, 31, 31, 43, 43, 43, 43, 43, 43, 43, 43, 3, 3, 1, 1, 1, 31, 31, 120, 120, 31, 31, 43, 43, 43, 43] 201 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 488 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517866 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(OCC(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 31, 43, 43, 43, 43, 11, 17, 17, 21, 21, 17, 19, 79, 128, 137, 137, 21, 21, 1, 1, 1, 2, 2, 2, 1, 1, 31, 31, 43, 43, 43, 21, 21, 128, 128, 21, 21, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 44, 25, 26, 27, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47]) total number of confs: 573 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517866 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(OCC(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 20, 21, 21, 12, 6, 12, 25, 31, 31, 31, 31, 1, 6, 1, 1, 1, 1, 1, 6, 18, 27, 27, 1, 1, 21, 21, 21, 21, 21, 21, 21, 21, 25, 25, 31, 31, 31, 1, 1, 18, 18, 1, 1, 21, 21, 21, 21] 201 rigid atoms, others: [38, 39, 42, 43, 12, 14, 15, 16, 17, 18, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 44, 45, 46, 47]) total number of confs: 204 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517866 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517866 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517866/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517866 Building REAL300004517867 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517867' /scratch/stefan/7774842/working/building/REAL300004517867 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517867 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517867/0 /scratch/stefan/7774842/working/building/REAL300004517867 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 909) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/909 `/scratch/stefan/7774842/working/3D/909' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)CCSCC(=O)[O-])C=C1C) `REAL300004517867.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517867.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517867/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517867 none CC1=CC=C(N(CC2=CC=CO2)C(=O)CCSCC(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 5, 14, 5, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 53, 53, 13, 4, 1, 1, 1, 1, 1, 1, 13, 24, 24, 50, 57, 98, 107, 107, 107, 53, 53, 53, 53, 53, 53, 53, 53, 4, 4, 1, 1, 1, 50, 50, 57, 57, 107, 107, 53, 53, 53, 53] 201 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 649 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517867 none CC1=CC=C(N(CC2=CC=CO2)C(=O)CCSCC(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 5, 14, 5, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 25, 53, 53, 53, 53, 7, 13, 13, 29, 41, 83, 111, 115, 115, 1, 1, 1, 2, 2, 2, 1, 1, 25, 25, 53, 53, 53, 29, 29, 41, 41, 111, 111, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 40, 21, 22, 23, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43]) total number of confs: 568 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517867 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517867 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517867/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517867 Building REAL300004517868 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517868' /scratch/stefan/7774842/working/building/REAL300004517868 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517868 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517868/0 /scratch/stefan/7774842/working/building/REAL300004517868 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 910) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/910 `/scratch/stefan/7774842/working/3D/910' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(C(=O)[O-])C=N2)C=C1C) `REAL300004517868.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517868.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517868/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517868 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(C(=O)[O-])C=N2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [96, 67, 96, 96, 25, 5, 1, 1, 1, 1, 1, 1, 25, 71, 71, 97, 97, 97, 97, 97, 97, 97, 97, 96, 96, 96, 96, 96, 96, 96, 96, 5, 5, 1, 1, 1, 97, 97, 97, 96, 96, 96, 96] 201 rigid atoms, others: [33, 34, 35, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 469 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517868 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(C(=O)[O-])C=N2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 46, 96, 96, 96, 96, 11, 31, 31, 73, 73, 73, 73, 73, 73, 73, 73, 1, 1, 1, 2, 2, 2, 1, 1, 46, 46, 96, 96, 96, 73, 73, 73, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 39, 23, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42]) total number of confs: 376 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517868 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(C(=O)[O-])C=N2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 57, 73, 73, 23, 9, 23, 59, 97, 97, 97, 97, 1, 9, 1, 1, 1, 1, 1, 2, 2, 1, 1, 73, 73, 73, 73, 73, 73, 73, 73, 59, 59, 97, 97, 97, 1, 1, 1, 73, 73, 73, 73] 201 rigid atoms, others: [36, 37, 38, 12, 14, 15, 16, 17, 18, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42]) total number of confs: 443 number of broken/clashed sets: 6 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517868 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517868 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517868/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517868 Building REAL300004517869 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517869' /scratch/stefan/7774842/working/building/REAL300004517869 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517869 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517869/0 /scratch/stefan/7774842/working/building/REAL300004517869 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 911) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/911 `/scratch/stefan/7774842/working/3D/911' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)COCC(=O)[O-])C=C1C) `REAL300004517869.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517869.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517869/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517869 none CC1=CC=C(N(CC2=CC=CO2)C(=O)COCC(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 12, 5, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 46, 46, 15, 4, 1, 1, 1, 1, 1, 1, 15, 25, 25, 72, 113, 121, 122, 122, 46, 46, 46, 46, 46, 46, 46, 46, 4, 4, 1, 1, 1, 72, 72, 121, 121, 46, 46, 46, 46] 201 rigid atoms, others: [32, 6, 7, 8, 9, 10, 11, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 616 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517869 none CC1=CC=C(N(CC2=CC=CO2)C(=O)COCC(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 12, 5, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 10, 30, 46, 46, 46, 46, 10, 18, 18, 59, 110, 123, 131, 131, 1, 1, 1, 2, 2, 2, 1, 1, 30, 30, 46, 46, 46, 59, 59, 123, 123, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 20, 21, 22, 26, 27, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 25, 28, 29, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40]) total number of confs: 511 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517869 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517869 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517869/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517869 Building REAL300004517870 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517870' /scratch/stefan/7774842/working/building/REAL300004517870 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517870 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517870/0 /scratch/stefan/7774842/working/building/REAL300004517870 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 912) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/912 `/scratch/stefan/7774842/working/3D/912' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC(C(=O)[O-])=NN2C)C=C1C) `REAL300004517870.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517870.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517870/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517870 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC(C(=O)[O-])=NN2C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 11, 11, 8, 8, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 96, 96, 22, 5, 1, 1, 1, 1, 1, 1, 22, 60, 60, 102, 102, 102, 102, 102, 102, 102, 102, 96, 96, 96, 94, 96, 96, 96, 96, 5, 5, 1, 1, 1, 102, 102, 102, 102, 96, 96, 96, 96] 201 rigid atoms, others: [33, 34, 35, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 722 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517870 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC(C(=O)[O-])=NN2C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 11, 11, 8, 8, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 43, 96, 96, 96, 96, 11, 28, 28, 68, 68, 68, 68, 68, 68, 68, 68, 1, 1, 1, 2, 2, 2, 1, 1, 43, 43, 96, 96, 96, 68, 68, 68, 68, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 40, 23, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43]) total number of confs: 363 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517870 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC(C(=O)[O-])=NN2C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 11, 11, 8, 8, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 68, 68, 21, 9, 21, 62, 102, 102, 102, 102, 1, 9, 1, 1, 1, 1, 2, 2, 1, 1, 1, 68, 68, 68, 68, 68, 68, 68, 68, 62, 62, 102, 102, 102, 1, 2, 2, 2, 68, 68, 68, 68] 201 rigid atoms, others: [36, 12, 14, 15, 16, 17, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 18, 19, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 660 number of broken/clashed sets: 8 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517870 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517870 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517870/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517870 Building REAL300004517871 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517871' /scratch/stefan/7774842/working/building/REAL300004517871 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517871 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517871/0 /scratch/stefan/7774842/working/building/REAL300004517871 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 913) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/913 `/scratch/stefan/7774842/working/3D/913' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@H]2C[C@@H](C)[C@H](C(=O)[O-])O2)C=C1C) `REAL300004517871.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517871.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517871/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517871 none CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@H]2C[C@@H](C)[C@H](C(=O)[O-])O2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 7, 5, 5, 7, 5, 5, 7, 1, 11, 11, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 87, 87, 23, 5, 1, 1, 1, 1, 1, 1, 23, 52, 52, 93, 93, 93, 93, 93, 93, 93, 93, 108, 108, 93, 87, 87, 87, 87, 87, 87, 87, 87, 5, 5, 1, 1, 1, 93, 93, 93, 93, 93, 87, 87, 87, 87] 201 rigid atoms, others: [36, 37, 6, 7, 8, 9, 10, 11, 38] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 782 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517871 none CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@H]2C[C@@H](C)[C@H](C(=O)[O-])O2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 7, 5, 5, 7, 5, 5, 7, 1, 11, 11, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 42, 87, 87, 87, 87, 11, 29, 29, 63, 63, 63, 63, 63, 63, 63, 63, 94, 94, 63, 1, 1, 1, 2, 2, 2, 1, 1, 42, 42, 87, 87, 87, 63, 63, 63, 63, 63, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 44, 26, 27, 28, 5] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47]) total number of confs: 520 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517871 none CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@H]2C[C@@H](C)[C@H](C(=O)[O-])O2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 7, 5, 5, 7, 5, 5, 7, 1, 11, 11, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [22, 22, 63, 63, 22, 7, 22, 61, 93, 93, 93, 93, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 63, 63, 63, 63, 63, 63, 63, 63, 61, 61, 93, 93, 93, 1, 1, 2, 2, 2, 63, 63, 63, 63] 201 rigid atoms, others: [39, 40, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 615 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517871 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517871 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517871/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517871 Building REAL300004517872 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517872' /scratch/stefan/7774842/working/building/REAL300004517872 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517872 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517872/0 /scratch/stefan/7774842/working/building/REAL300004517872 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 914) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/914 `/scratch/stefan/7774842/working/3D/914' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(CC(=O)[O-])C=C2)C=C1C) `REAL300004517872.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517872.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517872/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517872 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(CC(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 93, 93, 25, 4, 1, 1, 1, 1, 1, 1, 25, 57, 57, 77, 77, 64, 64, 108, 111, 111, 77, 77, 93, 93, 93, 91, 92, 92, 93, 93, 4, 4, 1, 1, 1, 77, 77, 108, 108, 77, 77, 93, 93, 93, 93] 201 rigid atoms, others: [34, 35, 36, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 943 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517872 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(CC(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 45, 93, 93, 93, 93, 11, 35, 35, 46, 46, 39, 39, 68, 90, 90, 46, 46, 1, 1, 1, 2, 2, 2, 1, 1, 45, 45, 93, 93, 93, 46, 46, 68, 68, 46, 46, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 43, 24, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46]) total number of confs: 594 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517872 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(CC(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 46, 46, 17, 6, 17, 51, 77, 77, 77, 77, 1, 6, 1, 1, 1, 1, 1, 2, 7, 7, 1, 1, 46, 46, 46, 46, 46, 46, 46, 46, 51, 51, 77, 77, 77, 1, 1, 2, 2, 1, 1, 46, 46, 46, 46] 201 rigid atoms, others: [37, 38, 41, 42, 12, 14, 15, 16, 17, 18, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 43, 44, 45, 46]) total number of confs: 492 number of broken/clashed sets: 6 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517872 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517872 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517872/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517872 Building REAL300004517873 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517873' /scratch/stefan/7774842/working/building/REAL300004517873 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517873 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517873/0 /scratch/stefan/7774842/working/building/REAL300004517873 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 915) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/915 `/scratch/stefan/7774842/working/3D/915' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(C=CC(=O)[O-])C=C2)C=C1C) `REAL300004517873.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517873.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517873/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517873 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(C=CC(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 41, 71, 71, 19, 5, 1, 1, 1, 1, 1, 1, 19, 40, 40, 57, 57, 40, 40, 108, 108, 109, 109, 57, 57, 71, 71, 71, 71, 71, 71, 71, 71, 5, 5, 1, 1, 1, 57, 57, 108, 108, 57, 57, 71, 71, 71, 71] 201 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 589 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517873 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(C=CC(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 39, 71, 71, 71, 71, 11, 21, 21, 28, 28, 21, 21, 82, 82, 103, 103, 28, 28, 1, 1, 1, 2, 2, 2, 1, 1, 39, 39, 71, 71, 71, 28, 28, 82, 82, 28, 28, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 44, 25, 26, 27, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47]) total number of confs: 518 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517873 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(C=CC(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [28, 25, 28, 28, 13, 6, 13, 37, 57, 57, 57, 57, 1, 6, 1, 1, 1, 1, 1, 5, 5, 11, 11, 1, 1, 28, 28, 28, 28, 28, 28, 28, 28, 37, 37, 57, 57, 57, 1, 1, 5, 5, 1, 1, 28, 28, 28, 28] 201 rigid atoms, others: [38, 39, 42, 43, 12, 14, 15, 16, 17, 18, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 44, 45, 46, 47]) total number of confs: 246 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517873 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517873 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517873/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517873 Building REAL300004517874 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517874' /scratch/stefan/7774842/working/building/REAL300004517874 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517874 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517874/0 /scratch/stefan/7774842/working/building/REAL300004517874 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 916) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/916 `/scratch/stefan/7774842/working/3D/916' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)C=CC2=CC(C(=O)[O-])=CO2)C=C1C) `REAL300004517874.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517874.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517874/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517874 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C=CC2=CC(C(=O)[O-])=CO2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 61, 61, 14, 4, 1, 1, 1, 1, 1, 1, 14, 29, 29, 89, 89, 143, 143, 143, 143, 143, 143, 143, 61, 61, 61, 59, 61, 61, 61, 61, 4, 4, 1, 1, 1, 89, 89, 143, 143, 61, 61, 61, 61] 201 rigid atoms, others: [34, 35, 36, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 636 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517874 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C=CC2=CC(C(=O)[O-])=CO2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 37, 61, 61, 61, 61, 11, 19, 19, 57, 57, 117, 117, 117, 117, 117, 117, 117, 1, 1, 1, 2, 2, 2, 1, 1, 37, 37, 61, 61, 61, 57, 57, 117, 117, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 41, 24, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44]) total number of confs: 411 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517874 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C=CC2=CC(C(=O)[O-])=CO2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 117, 117, 60, 34, 60, 117, 143, 143, 143, 143, 11, 33, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 117, 117, 117, 117, 117, 117, 117, 117, 117, 117, 143, 143, 143, 11, 11, 1, 1, 117, 117, 117, 117] 201 rigid atoms, others: [39, 40, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44]) total number of confs: 1044 number of broken/clashed sets: 5 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517874 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517874 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517874/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517874 Building REAL300004517875 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517875' /scratch/stefan/7774842/working/building/REAL300004517875 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517875 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517875/0 /scratch/stefan/7774842/working/building/REAL300004517875 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 917) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/917 `/scratch/stefan/7774842/working/3D/917' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)COCC2=C(C(=O)[O-])N=CO2)C=C1C) `REAL300004517875.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517875/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517875 none CC1=CC=C(N(CC2=CC=CO2)C(=O)COCC2=C(C(=O)[O-])N=CO2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 12, 5, 1, 1, 1, 11, 11, 8, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 114 conformations in input total number of sets (complete confs): 114 using faster count positions algorithm for large data unique positions, atoms: [12, 12, 32, 32, 12, 4, 1, 1, 1, 1, 1, 1, 12, 21, 21, 41, 54, 66, 66, 66, 66, 66, 66, 66, 66, 32, 32, 32, 32, 32, 32, 32, 32, 4, 4, 1, 1, 1, 41, 41, 66, 66, 66, 32, 32, 32, 32] 114 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 388 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517875 none CC1=CC=C(N(CC2=CC=CO2)C(=O)COCC2=C(C(=O)[O-])N=CO2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 12, 5, 1, 1, 1, 11, 11, 8, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 114 conformations in input total number of sets (complete confs): 114 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 21, 32, 32, 32, 32, 9, 17, 17, 51, 72, 88, 88, 88, 88, 88, 88, 88, 88, 1, 1, 1, 2, 2, 2, 1, 1, 21, 21, 32, 32, 32, 51, 51, 88, 88, 88, 1, 2, 2, 2] 114 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 43, 25, 26, 27, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46]) total number of confs: 409 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517875 none CC1=CC=C(N(CC2=CC=CO2)C(=O)COCC2=C(C(=O)[O-])N=CO2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 12, 5, 1, 1, 1, 11, 11, 8, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 114 conformations in input total number of sets (complete confs): 114 using faster count positions algorithm for large data unique positions, atoms: [45, 45, 88, 88, 45, 29, 45, 62, 66, 66, 66, 66, 10, 29, 6, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 88, 88, 88, 88, 88, 88, 88, 88, 62, 62, 66, 66, 66, 10, 10, 3, 3, 1, 88, 88, 88, 88] 114 rigid atoms, others: [42, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45, 46]) total number of confs: 673 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517875 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517875 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517875/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517875 Building REAL300004517876 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517876' /scratch/stefan/7774842/working/building/REAL300004517876 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517876 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517876/0 /scratch/stefan/7774842/working/building/REAL300004517876 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 918) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/918 `/scratch/stefan/7774842/working/3D/918' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)C=CC2=CC=C(C(=O)[O-])O2)C=C1C) `REAL300004517876.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517876.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517876/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517876 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C=CC2=CC=C(C(=O)[O-])O2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [44, 21, 78, 78, 21, 4, 1, 1, 1, 1, 1, 1, 21, 49, 49, 104, 104, 134, 134, 134, 134, 134, 134, 134, 78, 78, 78, 78, 78, 78, 78, 78, 4, 4, 1, 1, 1, 104, 104, 134, 134, 78, 78, 78, 78] 201 rigid atoms, others: [34, 35, 36, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 732 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517876 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C=CC2=CC=C(C(=O)[O-])O2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 45, 78, 78, 78, 78, 11, 24, 24, 74, 74, 115, 115, 115, 115, 115, 115, 115, 1, 1, 1, 2, 2, 2, 1, 1, 45, 45, 78, 78, 78, 74, 74, 115, 115, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 41, 24, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44]) total number of confs: 480 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517876 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C=CC2=CC=C(C(=O)[O-])O2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [94, 49, 115, 115, 49, 24, 49, 103, 134, 134, 134, 134, 6, 23, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 115, 115, 115, 115, 115, 115, 115, 115, 103, 103, 134, 134, 134, 6, 6, 1, 1, 115, 115, 115, 115] 201 rigid atoms, others: [39, 40, 15, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 41, 42, 43, 44]) total number of confs: 907 number of broken/clashed sets: 9 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517876 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517876 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517876/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517876 Building REAL300004517877 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517877' /scratch/stefan/7774842/working/building/REAL300004517877 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517877 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517877/0 /scratch/stefan/7774842/working/building/REAL300004517877 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 919) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/919 `/scratch/stefan/7774842/working/3D/919' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@H]2CC[C@@H](C(=O)[O-])C2)C=C1C) `REAL300004517877.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517877/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517877 none CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@H]2CC[C@@H](C(=O)[O-])C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 11, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 37, 93, 93, 23, 5, 1, 1, 1, 1, 1, 1, 23, 53, 53, 103, 103, 103, 103, 103, 103, 108, 108, 103, 93, 93, 93, 93, 93, 93, 93, 93, 5, 5, 1, 1, 1, 103, 103, 103, 103, 103, 103, 93, 93, 93, 93] 201 rigid atoms, others: [34, 35, 36, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 806 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517877 none CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@H]2CC[C@@H](C(=O)[O-])C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 11, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 42, 93, 93, 93, 93, 11, 25, 25, 48, 48, 48, 48, 48, 48, 73, 73, 48, 1, 1, 1, 2, 2, 2, 1, 1, 42, 42, 93, 93, 93, 48, 48, 48, 48, 48, 48, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 43, 24, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46]) total number of confs: 458 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517877 none CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@H]2CC[C@@H](C(=O)[O-])C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 11, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 35, 48, 48, 19, 6, 19, 59, 103, 103, 103, 103, 1, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 48, 48, 48, 48, 48, 48, 48, 48, 59, 59, 103, 103, 103, 1, 1, 1, 1, 1, 1, 48, 48, 48, 48] 201 rigid atoms, others: [37, 38, 39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 43, 44, 45, 46]) total number of confs: 528 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517877 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517877 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517877/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517877 Building REAL300004517878 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517878' /scratch/stefan/7774842/working/building/REAL300004517878 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517878 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517878/0 /scratch/stefan/7774842/working/building/REAL300004517878 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 920) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/920 `/scratch/stefan/7774842/working/3D/920' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(C)C(C(=O)[O-])=C2)C=C1C) `REAL300004517878.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517878/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517878 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(C)C(C(=O)[O-])=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [88, 55, 88, 88, 25, 5, 1, 1, 1, 1, 1, 1, 25, 53, 53, 100, 100, 100, 100, 100, 100, 100, 100, 100, 88, 88, 88, 88, 88, 88, 88, 88, 5, 5, 1, 1, 1, 100, 100, 100, 100, 100, 100, 88, 88, 88, 88] 201 rigid atoms, others: [34, 35, 36, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 446 number of broken/clashed sets: 6 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517878 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(C)C(C(=O)[O-])=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 45, 88, 88, 88, 88, 11, 35, 35, 86, 86, 86, 86, 86, 86, 86, 86, 86, 1, 1, 1, 2, 2, 2, 1, 1, 45, 45, 88, 88, 88, 86, 86, 86, 86, 86, 86, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 43, 24, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46]) total number of confs: 390 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517878 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(C)C(C(=O)[O-])=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [86, 69, 86, 86, 31, 11, 31, 82, 100, 100, 100, 100, 1, 11, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 86, 86, 86, 86, 86, 86, 86, 86, 82, 82, 100, 100, 100, 1, 1, 2, 2, 2, 1, 86, 86, 86, 86] 201 rigid atoms, others: [37, 38, 42, 12, 14, 15, 16, 17, 18, 19, 20, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 43, 44, 45, 46]) total number of confs: 512 number of broken/clashed sets: 6 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517878 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517878 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517878/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517878 Building REAL300004517879 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517879' /scratch/stefan/7774842/working/building/REAL300004517879 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517879 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517879/0 /scratch/stefan/7774842/working/building/REAL300004517879 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 921) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/921 `/scratch/stefan/7774842/working/3D/921' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CN=CC(C(=O)[O-])=C2)C=C1C) `REAL300004517879.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517879.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517879/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517879 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CN=CC(C(=O)[O-])=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [94, 49, 94, 94, 23, 5, 1, 1, 1, 1, 1, 1, 23, 45, 45, 106, 106, 106, 106, 106, 106, 106, 106, 94, 94, 94, 94, 94, 94, 94, 94, 5, 5, 1, 1, 1, 106, 106, 106, 94, 94, 94, 94] 201 rigid atoms, others: [33, 34, 35, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 478 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517879 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CN=CC(C(=O)[O-])=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 43, 94, 94, 94, 94, 11, 23, 23, 69, 69, 69, 69, 69, 69, 69, 69, 1, 1, 1, 2, 2, 2, 1, 1, 43, 43, 94, 94, 94, 69, 69, 69, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 39, 23, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42]) total number of confs: 348 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517879 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CN=CC(C(=O)[O-])=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [69, 49, 69, 69, 25, 11, 25, 69, 106, 106, 106, 106, 1, 11, 1, 1, 1, 1, 1, 1, 2, 2, 1, 69, 69, 69, 69, 69, 69, 69, 69, 69, 69, 106, 106, 106, 1, 1, 1, 69, 69, 69, 69] 201 rigid atoms, others: [36, 37, 38, 12, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42]) total number of confs: 499 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517879 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517879 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517879/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517879 Building REAL300004517880 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517880' /scratch/stefan/7774842/working/building/REAL300004517880 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517880 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517880/0 /scratch/stefan/7774842/working/building/REAL300004517880 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 922) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/922 `/scratch/stefan/7774842/working/3D/922' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC(C(=O)[O-])=CN=C2C)C=C1C) `REAL300004517880.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517880 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC(C(=O)[O-])=CN=C2C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 11, 11, 1, 8, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [85, 50, 85, 85, 23, 4, 1, 1, 1, 1, 1, 1, 23, 65, 65, 102, 102, 102, 102, 102, 102, 102, 102, 102, 85, 85, 85, 85, 85, 85, 85, 85, 4, 4, 1, 1, 1, 102, 102, 102, 102, 102, 85, 85, 85, 85] 201 rigid atoms, others: [34, 35, 36, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 456 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517880 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC(C(=O)[O-])=CN=C2C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 11, 11, 1, 8, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 45, 85, 85, 85, 85, 11, 36, 36, 71, 71, 71, 71, 71, 71, 71, 71, 71, 1, 1, 1, 2, 2, 2, 1, 1, 45, 45, 85, 85, 85, 71, 71, 71, 71, 71, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 42, 24, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45]) total number of confs: 360 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517880 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC(C(=O)[O-])=CN=C2C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 11, 11, 1, 8, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [71, 49, 71, 71, 21, 9, 21, 65, 102, 102, 102, 102, 1, 9, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 71, 71, 71, 71, 71, 71, 71, 71, 65, 65, 102, 102, 102, 1, 1, 2, 2, 2, 71, 71, 71, 71] 201 rigid atoms, others: [37, 38, 12, 14, 15, 16, 17, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 493 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517880 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517880 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517880/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517880 Building REAL300004517881 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517881' /scratch/stefan/7774842/working/building/REAL300004517881 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517881 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517881/0 /scratch/stefan/7774842/working/building/REAL300004517881 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 923) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/923 `/scratch/stefan/7774842/working/3D/923' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)CN2C=CC(C(=O)[O-])=N2)C=C1C) `REAL300004517881.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517881 none CC1=CC=C(N(CC2=CC=CO2)C(=O)CN2C=CC(C(=O)[O-])=N2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 8, 1, 1, 1, 1, 11, 11, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 47, 47, 15, 3, 1, 1, 1, 1, 1, 1, 15, 29, 29, 77, 112, 112, 112, 112, 112, 112, 112, 47, 47, 47, 47, 47, 47, 47, 47, 3, 3, 1, 1, 1, 77, 77, 112, 112, 47, 47, 47, 47] 201 rigid atoms, others: [33, 34, 35, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 402 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517881 none CC1=CC=C(N(CC2=CC=CO2)C(=O)CN2C=CC(C(=O)[O-])=N2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 8, 1, 1, 1, 1, 11, 11, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 29, 47, 47, 47, 47, 7, 15, 15, 47, 93, 93, 93, 93, 93, 93, 93, 1, 1, 1, 2, 2, 2, 1, 1, 29, 29, 47, 47, 47, 47, 47, 93, 93, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 40, 23, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43]) total number of confs: 359 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517881 none CC1=CC=C(N(CC2=CC=CO2)C(=O)CN2C=CC(C(=O)[O-])=N2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 8, 1, 1, 1, 1, 11, 11, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [93, 93, 93, 93, 43, 23, 43, 89, 112, 112, 112, 112, 6, 23, 1, 1, 1, 1, 1, 1, 2, 2, 1, 93, 93, 93, 93, 93, 93, 93, 93, 89, 89, 112, 112, 112, 6, 6, 1, 1, 93, 93, 93, 93] 201 rigid atoms, others: [38, 39, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 498 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517881 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517881 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517881/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517881 Building REAL300004517882 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517882' /scratch/stefan/7774842/working/building/REAL300004517882 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517882 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517882/0 /scratch/stefan/7774842/working/building/REAL300004517882 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 924) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/924 `/scratch/stefan/7774842/working/3D/924' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)CCCN2C=CC(C(=O)[O-])=N2)C=C1C) `REAL300004517882.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517882/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517882 none CC1=CC=C(N(CC2=CC=CO2)C(=O)CCCN2C=CC(C(=O)[O-])=N2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 5, 5, 8, 1, 1, 1, 1, 11, 11, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [41, 21, 72, 72, 21, 4, 1, 1, 1, 1, 1, 1, 21, 38, 38, 48, 48, 48, 50, 50, 50, 50, 50, 50, 50, 72, 72, 72, 72, 72, 72, 72, 72, 4, 4, 1, 1, 1, 48, 48, 48, 48, 48, 48, 50, 50, 72, 72, 72, 72] 108 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 507 number of broken/clashed sets: 55 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517882 none CC1=CC=C(N(CC2=CC=CO2)C(=O)CCCN2C=CC(C(=O)[O-])=N2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 5, 5, 8, 1, 1, 1, 1, 11, 11, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 41, 72, 72, 72, 72, 9, 17, 17, 45, 45, 45, 53, 53, 53, 53, 53, 53, 53, 1, 1, 1, 2, 2, 2, 1, 1, 41, 41, 72, 72, 72, 45, 45, 45, 45, 45, 45, 53, 53, 1, 2, 2, 2] 108 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 46, 25, 26, 27, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49]) total number of confs: 380 number of broken/clashed sets: 55 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517882 none CC1=CC=C(N(CC2=CC=CO2)C(=O)CCCN2C=CC(C(=O)[O-])=N2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 5, 5, 8, 1, 1, 1, 1, 11, 11, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [41, 21, 53, 53, 21, 15, 21, 43, 50, 50, 50, 50, 7, 15, 7, 6, 1, 1, 1, 1, 1, 1, 2, 2, 1, 53, 53, 53, 53, 53, 53, 53, 53, 43, 43, 50, 50, 50, 7, 7, 7, 7, 6, 6, 1, 1, 53, 53, 53, 53] 108 rigid atoms, others: [44, 45, 16, 17, 18, 19, 20, 21, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48, 49]) total number of confs: 403 number of broken/clashed sets: 55 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517882 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517882 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517882/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517882 Building REAL300004517883 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517883' /scratch/stefan/7774842/working/building/REAL300004517883 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517883 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517883/0 /scratch/stefan/7774842/working/building/REAL300004517883 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 925) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/925 `/scratch/stefan/7774842/working/3D/925' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@H]2CC[C@H]2C(=O)[O-])C=C1C) `REAL300004517883.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517883.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517883/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517883 none CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@H]2CC[C@H]2C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 74, 74, 21, 5, 1, 1, 1, 1, 1, 1, 21, 34, 34, 40, 40, 40, 40, 40, 40, 41, 41, 74, 74, 74, 74, 72, 74, 74, 74, 4, 4, 1, 1, 1, 40, 40, 40, 40, 74, 74, 74, 74] 81 rigid atoms, others: [33, 34, 35, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 505 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517883 none CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@H]2CC[C@H]2C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 38, 74, 74, 74, 74, 11, 21, 21, 27, 27, 27, 27, 27, 27, 29, 29, 1, 1, 1, 2, 2, 2, 1, 1, 38, 38, 74, 74, 74, 27, 27, 27, 27, 1, 2, 2, 2] 81 rigid atoms, others: [0, 1, 2, 3, 4, 5, 40, 23, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43]) total number of confs: 274 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517883 none CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@H]2CC[C@H]2C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 27, 27, 8, 3, 8, 24, 40, 40, 40, 40, 1, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 27, 27, 27, 27, 27, 27, 27, 27, 24, 24, 40, 40, 40, 1, 1, 1, 1, 27, 27, 27, 27] 81 rigid atoms, others: [36, 37, 38, 39, 12, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43]) total number of confs: 260 number of broken/clashed sets: 15 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517883 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517883 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517883/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517883 Building REAL300004517884 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517884' /scratch/stefan/7774842/working/building/REAL300004517884 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517884 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517884/0 /scratch/stefan/7774842/working/building/REAL300004517884 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 926) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/926 `/scratch/stefan/7774842/working/3D/926' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@H]2CC[C@@H](CCC(=O)[O-])O2)C=C1C) `REAL300004517884.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517884.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517884/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517884 none CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@H]2CC[C@@H](CCC(=O)[O-])O2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 7, 5, 5, 5, 7, 5, 5, 1, 11, 11, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [69, 41, 69, 69, 19, 5, 1, 1, 1, 1, 1, 1, 19, 42, 42, 66, 66, 66, 66, 66, 66, 118, 121, 124, 124, 66, 69, 69, 69, 69, 69, 69, 69, 69, 5, 5, 1, 1, 1, 66, 66, 66, 66, 118, 118, 121, 121, 69, 69, 69, 69] 201 rigid atoms, others: [36, 37, 6, 7, 8, 9, 10, 11, 38] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 675 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517884 none CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@H]2CC[C@@H](CCC(=O)[O-])O2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 7, 5, 5, 5, 7, 5, 5, 1, 11, 11, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 41, 69, 69, 69, 69, 11, 26, 26, 45, 45, 45, 45, 45, 45, 101, 106, 116, 116, 45, 1, 1, 1, 2, 2, 2, 1, 1, 41, 41, 69, 69, 69, 45, 45, 45, 45, 101, 101, 106, 106, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 47, 26, 27, 28, 5] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50]) total number of confs: 645 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517884 none CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@H]2CC[C@@H](CCC(=O)[O-])O2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 7, 5, 5, 5, 7, 5, 5, 1, 11, 11, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 36, 45, 45, 17, 7, 17, 48, 66, 66, 66, 66, 1, 7, 1, 1, 1, 1, 1, 1, 1, 6, 9, 11, 11, 1, 45, 45, 45, 45, 45, 45, 45, 45, 48, 48, 66, 66, 66, 1, 1, 1, 1, 6, 6, 9, 9, 45, 45, 45, 45] 201 rigid atoms, others: [39, 40, 41, 42, 12, 14, 15, 16, 17, 18, 19, 20, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 346 number of broken/clashed sets: 7 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517884 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517884 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517884/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517884 Building REAL300004517885 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517885' /scratch/stefan/7774842/working/building/REAL300004517885 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517885 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517885/0 /scratch/stefan/7774842/working/building/REAL300004517885 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 927) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/927 `/scratch/stefan/7774842/working/3D/927' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)CC[C@@H]2C[C@H](C(=O)[O-])CO2)C=C1C) `REAL300004517885.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517885.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517885/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517885 none CC1=CC=C(N(CC2=CC=CO2)C(=O)CC[C@@H]2C[C@H](C(=O)[O-])CO2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 5, 5, 7, 5, 5, 7, 1, 11, 11, 5, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [15, 15, 45, 45, 15, 4, 1, 1, 1, 1, 1, 1, 15, 23, 23, 61, 77, 99, 99, 99, 99, 99, 110, 110, 99, 99, 45, 45, 45, 45, 45, 45, 45, 45, 4, 4, 1, 1, 1, 61, 61, 83, 83, 99, 99, 99, 99, 45, 45, 45, 45] 201 rigid atoms, others: [36, 37, 6, 7, 8, 9, 10, 11, 38] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 706 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517885 none CC1=CC=C(N(CC2=CC=CO2)C(=O)CC[C@@H]2C[C@H](C(=O)[O-])CO2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 5, 5, 7, 5, 5, 7, 1, 11, 11, 5, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 30, 45, 45, 45, 45, 9, 13, 13, 45, 64, 102, 102, 102, 102, 102, 118, 118, 102, 102, 1, 1, 1, 2, 2, 2, 1, 1, 30, 30, 45, 45, 45, 45, 45, 72, 72, 102, 102, 102, 102, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 33, 32, 47, 26, 27, 28, 5] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50]) total number of confs: 632 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517885 none CC1=CC=C(N(CC2=CC=CO2)C(=O)CC[C@@H]2C[C@H](C(=O)[O-])CO2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 5, 5, 7, 5, 5, 7, 1, 11, 11, 5, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [44, 44, 102, 102, 44, 31, 44, 88, 99, 99, 99, 99, 10, 31, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 102, 102, 102, 102, 102, 102, 102, 102, 88, 88, 99, 99, 99, 10, 10, 6, 6, 1, 1, 1, 1, 102, 102, 102, 102] 201 rigid atoms, others: [43, 44, 45, 46, 15, 16, 17, 18, 19, 20, 21, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 47, 48, 49, 50]) total number of confs: 938 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517885 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517885 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517885/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517885 Building REAL300004517886 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517886' /scratch/stefan/7774842/working/building/REAL300004517886 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517886 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517886/0 /scratch/stefan/7774842/working/building/REAL300004517886 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 928) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/928 `/scratch/stefan/7774842/working/3D/928' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@H]2CC[C@H]2C(=O)[O-])C=C1C) `REAL300004517886.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517886.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517886/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517886 none CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@H]2CC[C@H]2C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 74, 74, 21, 5, 1, 1, 1, 1, 1, 1, 21, 34, 34, 40, 40, 40, 40, 40, 40, 41, 41, 74, 74, 74, 74, 72, 74, 74, 74, 4, 4, 1, 1, 1, 40, 40, 40, 40, 74, 74, 74, 74] 81 rigid atoms, others: [33, 34, 35, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 505 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517886 none CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@H]2CC[C@H]2C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 38, 74, 74, 74, 74, 11, 21, 21, 27, 27, 27, 27, 27, 27, 29, 29, 1, 1, 1, 2, 2, 2, 1, 1, 38, 38, 74, 74, 74, 27, 27, 27, 27, 1, 2, 2, 2] 81 rigid atoms, others: [0, 1, 2, 3, 4, 5, 40, 23, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43]) total number of confs: 274 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517886 none CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@H]2CC[C@H]2C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 81 conformations in input total number of sets (complete confs): 81 using faster count positions algorithm for large data unique positions, atoms: [8, 8, 27, 27, 8, 3, 8, 24, 40, 40, 40, 40, 1, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 27, 27, 27, 27, 27, 27, 27, 27, 24, 24, 40, 40, 40, 1, 1, 1, 1, 27, 27, 27, 27] 81 rigid atoms, others: [36, 37, 38, 39, 12, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43]) total number of confs: 260 number of broken/clashed sets: 15 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517886 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517886 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517886/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517886 Building REAL300004517887 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517887' /scratch/stefan/7774842/working/building/REAL300004517887 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517887 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517887/0 /scratch/stefan/7774842/working/building/REAL300004517887 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 929) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/929 `/scratch/stefan/7774842/working/3D/929' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@H]2C[C@H]2C(=O)[O-])C=C1C) `REAL300004517887.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517887.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517887/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517887 none CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@H]2C[C@H]2C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 7, 5, 5, 7, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [39, 35, 75, 75, 20, 4, 1, 1, 1, 1, 1, 1, 19, 37, 37, 46, 46, 46, 46, 46, 52, 52, 75, 75, 75, 75, 74, 75, 75, 75, 4, 4, 1, 1, 1, 46, 46, 75, 75, 75, 75] 103 rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40]) total number of confs: 477 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517887 none CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@H]2C[C@H]2C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 7, 5, 5, 7, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 36, 75, 75, 75, 75, 11, 34, 34, 44, 44, 44, 44, 44, 50, 50, 1, 1, 1, 2, 2, 2, 1, 1, 36, 36, 75, 75, 75, 44, 44, 1, 2, 2, 2] 103 rigid atoms, others: [0, 1, 2, 3, 4, 5, 22, 23, 24, 28, 29, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40]) total number of confs: 328 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517887 none CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@H]2C[C@H]2C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 7, 5, 5, 7, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 103 conformations in input total number of sets (complete confs): 103 using faster count positions algorithm for large data unique positions, atoms: [23, 21, 44, 44, 12, 6, 12, 29, 46, 46, 46, 46, 1, 6, 1, 1, 1, 1, 1, 1, 3, 3, 44, 44, 44, 44, 44, 44, 44, 44, 29, 29, 46, 46, 46, 1, 1, 44, 44, 44, 44] 103 rigid atoms, others: [35, 36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40]) total number of confs: 330 number of broken/clashed sets: 5 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517887 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517887 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517887/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517887 Building REAL300004517888 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517888' /scratch/stefan/7774842/working/building/REAL300004517888 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517888 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517888/0 /scratch/stefan/7774842/working/building/REAL300004517888 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 930) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/930 `/scratch/stefan/7774842/working/3D/930' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)N(CC2=CC=CO2)C2=CC=C(C)C(C)=C2)OC(C(=O)[O-])=C1) `REAL300004517888.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517888.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517888/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517888 none CC1=C(C(=O)N(CC2=CC=CO2)C2=CC=C(C)C(C)=C2)OC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 1, 5, 1, 12, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [97, 97, 62, 25, 62, 5, 1, 1, 1, 1, 1, 1, 25, 84, 84, 25, 25, 84, 84, 84, 97, 97, 97, 97, 97, 97, 97, 97, 97, 5, 5, 1, 1, 1, 84, 84, 82, 84, 84, 84, 84, 84, 84, 97] 201 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 665 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517888 none CC1=C(C(=O)N(CC2=CC=CO2)C2=CC=C(C)C(C)=C2)OC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 1, 5, 1, 12, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 10, 10, 29, 64, 97, 97, 97, 97, 29, 105, 105, 29, 29, 105, 105, 105, 1, 1, 1, 2, 2, 1, 2, 2, 2, 64, 64, 97, 97, 97, 105, 105, 105, 105, 105, 105, 105, 105, 105, 1] 201 rigid atoms, others: [0, 1, 2, 3, 43, 20, 21, 22, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 841 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517888 none CC1=C(C(=O)N(CC2=CC=CO2)C2=CC=C(C)C(C)=C2)OC(C(=O)[O-])=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 1, 5, 1, 12, 1, 1, 11, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 41, 11, 41, 1, 11, 45, 84, 84, 84, 84, 1, 1, 1, 1, 1, 1, 1, 1, 105, 105, 105, 105, 105, 105, 105, 105, 105, 45, 45, 84, 84, 84, 1, 1, 2, 2, 2, 2, 2, 2, 1, 105] 201 rigid atoms, others: [34, 35, 5, 42, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 43]) total number of confs: 411 number of broken/clashed sets: 5 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517888 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517888 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517888/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517888 Building REAL300004517889 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517889' /scratch/stefan/7774842/working/building/REAL300004517889 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517889 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517889/0 /scratch/stefan/7774842/working/building/REAL300004517889 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 931) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/931 `/scratch/stefan/7774842/working/3D/931' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@@H]2C3C=CC(CC3)[C@@H]2C(=O)[O-])C=C1C) `REAL300004517889.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517889.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517889/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517889 none CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@@H]2C3C=CC(CC3)[C@@H]2C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 7, 5, 1, 1, 5, 5, 5, 5, 7, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [20, 11, 28, 28, 11, 5, 1, 1, 1, 1, 1, 1, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 28, 28, 28, 28, 28, 28, 28, 28, 5, 5, 1, 1, 1, 15, 15, 15, 15, 15, 15, 15, 15, 28, 28, 28, 28] 28 rigid atoms, others: [37, 6, 7, 8, 9, 10, 11, 39, 38] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 175 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517889 none CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@@H]2C3C=CC(CC3)[C@@H]2C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 7, 5, 1, 1, 5, 5, 5, 5, 7, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 21, 28, 28, 28, 28, 11, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 1, 1, 1, 2, 2, 2, 1, 1, 21, 21, 28, 28, 28, 15, 15, 15, 15, 15, 15, 15, 15, 1, 2, 2, 2] 28 rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 34, 48, 27, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51]) total number of confs: 113 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517889 none CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@@H]2C3C=CC(CC3)[C@@H]2C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 7, 5, 1, 1, 5, 5, 5, 5, 7, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 28 conformations in input total number of sets (complete confs): 28 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 15, 15, 6, 3, 6, 10, 15, 15, 15, 15, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 15, 15, 15, 15, 15, 15, 15, 15, 10, 10, 15, 15, 15, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15] 28 rigid atoms, others: [24, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 46, 47, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 48, 49, 50, 51]) total number of confs: 103 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517889 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517889 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517889/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517889 Building REAL300004517890 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517890' /scratch/stefan/7774842/working/building/REAL300004517890 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517890 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517890/0 /scratch/stefan/7774842/working/building/REAL300004517890 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 932) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/932 `/scratch/stefan/7774842/working/3D/932' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C(=O)[O-])C(=O)N(CC1=CC=CO1)C1=CC=C(C)C(C)=C1) `REAL300004517890.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517890 none CCC(C(=O)[O-])C(=O)N(CC1=CC=CO1)C1=CC=C(C)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 11, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [45, 31, 15, 31, 44, 44, 7, 15, 1, 7, 35, 68, 68, 68, 68, 1, 1, 1, 1, 1, 1, 1, 1, 47, 47, 47, 47, 47, 31, 35, 35, 68, 68, 68, 1, 1, 2, 2, 2, 2, 2, 2, 1] 160 rigid atoms, others: [34, 35, 8, 42, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41]) total number of confs: 445 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517890 none CCC(C(=O)[O-])C(=O)N(CC1=CC=CO1)C1=CC=C(C)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 11, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 160 conformations in input total number of sets (complete confs): 160 using faster count positions algorithm for large data unique positions, atoms: [86, 72, 38, 72, 87, 87, 18, 38, 4, 1, 1, 1, 1, 1, 1, 18, 68, 68, 18, 18, 68, 68, 68, 86, 86, 86, 86, 86, 72, 4, 4, 1, 1, 1, 68, 68, 68, 68, 68, 68, 68, 68, 68] 160 rigid atoms, others: [32, 33, 9, 10, 11, 12, 13, 14, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 781 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517890 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517890 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517890/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517890 Building REAL300004517891 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517891' /scratch/stefan/7774842/working/building/REAL300004517891 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517891 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517891/0 /scratch/stefan/7774842/working/building/REAL300004517891 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 933) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/933 `/scratch/stefan/7774842/working/3D/933' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)C(C(=O)[O-])C(C)C)C=C1C) `REAL300004517891.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517891 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C(C(=O)[O-])C(C)C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 1, 11, 11, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 111, 111, 24, 5, 1, 1, 1, 1, 1, 1, 24, 68, 68, 86, 92, 92, 86, 95, 95, 111, 111, 111, 109, 111, 109, 111, 111, 5, 5, 1, 1, 1, 86, 95, 95, 95, 95, 95, 95, 95, 111, 111, 111, 111] 188 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 927 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517891 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C(C(=O)[O-])C(C)C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 1, 11, 11, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 49, 111, 111, 111, 111, 11, 29, 29, 47, 53, 53, 47, 58, 58, 1, 1, 1, 2, 2, 2, 1, 1, 49, 49, 111, 111, 111, 47, 58, 58, 58, 58, 58, 58, 58, 1, 2, 2, 2] 188 rigid atoms, others: [0, 1, 2, 3, 4, 5, 42, 21, 22, 23, 27, 28] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45]) total number of confs: 513 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517891 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517891 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517891/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517891 Building REAL300004517892 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517892' /scratch/stefan/7774842/working/building/REAL300004517892 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517892 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517892/0 /scratch/stefan/7774842/working/building/REAL300004517892 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 934) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/934 `/scratch/stefan/7774842/working/3D/934' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@H]2CCCC[C@H]2C(=O)[O-])C=C1C) `REAL300004517892.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517892 none CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@H]2CCCC[C@H]2C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 7, 5, 5, 5, 5, 5, 7, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 42, 42, 13, 4, 1, 1, 1, 1, 1, 1, 13, 20, 20, 29, 29, 29, 29, 29, 29, 29, 29, 30, 30, 42, 42, 42, 42, 42, 42, 42, 42, 4, 4, 1, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29, 42, 42, 42, 42] 57 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 316 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517892 none CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@H]2CCCC[C@H]2C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 7, 5, 5, 5, 5, 5, 7, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 25, 42, 42, 42, 42, 9, 16, 16, 24, 24, 24, 24, 24, 24, 24, 24, 26, 26, 1, 1, 1, 2, 2, 2, 1, 1, 25, 25, 42, 42, 42, 24, 24, 24, 24, 24, 24, 24, 24, 1, 2, 2, 2] 57 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 46, 25, 26, 27, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49]) total number of confs: 198 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517892 none CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@H]2CCCC[C@H]2C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 7, 5, 5, 5, 5, 5, 7, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 57 conformations in input total number of sets (complete confs): 57 using faster count positions algorithm for large data unique positions, atoms: [11, 11, 24, 24, 11, 4, 11, 21, 29, 29, 29, 29, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 24, 24, 24, 24, 24, 24, 24, 24, 21, 21, 29, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24] 57 rigid atoms, others: [38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 46, 47, 48, 49]) total number of confs: 213 number of broken/clashed sets: 5 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517892 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517892 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517892/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517892 Building REAL300004517893 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517893' /scratch/stefan/7774842/working/building/REAL300004517893 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300004517893 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517893/0 /scratch/stefan/7774842/working/building/REAL300004517893 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 935) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/935 `/scratch/stefan/7774842/working/3D/935' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)C[N@@H+]2CCCC(C(=O)[O-])C2)C=C1C) `REAL300004517893.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517893/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517893 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C[N@@H+]2CCCC(C(=O)[O-])C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 9, 6, 5, 5, 5, 5, 1, 11, 11, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 78, 78, 20, 4, 1, 1, 1, 1, 1, 1, 20, 43, 43, 90, 100, 100, 100, 100, 100, 100, 107, 107, 100, 78, 78, 78, 78, 77, 78, 78, 78, 4, 4, 1, 1, 1, 90, 90, 100, 100, 100, 100, 100, 100, 100, 100, 100, 78, 78, 78, 78] 201 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 794 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517893 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C[N@@H+]2CCCC(C(=O)[O-])C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 9, 6, 5, 5, 5, 5, 1, 11, 11, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 42, 78, 78, 78, 78, 11, 23, 23, 58, 84, 84, 84, 84, 84, 84, 109, 109, 84, 1, 1, 1, 2, 2, 2, 1, 1, 42, 42, 78, 78, 78, 58, 58, 84, 84, 84, 84, 84, 84, 84, 84, 84, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 49, 25, 26, 27, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52]) total number of confs: 599 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517893 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C[N@@H+]2CCCC(C(=O)[O-])C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 9, 6, 5, 5, 5, 5, 1, 11, 11, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [38, 38, 84, 84, 37, 19, 38, 85, 100, 100, 100, 100, 5, 19, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 84, 84, 84, 84, 84, 84, 84, 84, 85, 85, 100, 100, 100, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 84, 84, 84, 84] 201 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 24, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 795 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517893 /scratch/stefan/7774842/working /scratch/stefan/7774842 mkdir: created directory `1' /scratch/stefan/7774842/working/building/REAL300004517893/1 /scratch/stefan/7774842/working/building/REAL300004517893 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 1 (index: 936) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/936 `/scratch/stefan/7774842/working/3D/936' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)C[N@H+]2CCCC(C(=O)[O-])C2)C=C1C) `REAL300004517893.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004517893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517893/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517893 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C[N@H+]2CCCC(C(=O)[O-])C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 9, 6, 5, 5, 5, 5, 1, 11, 11, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 34, 67, 67, 19, 5, 1, 1, 1, 1, 1, 1, 19, 34, 34, 76, 92, 92, 92, 92, 92, 92, 106, 106, 92, 67, 67, 67, 67, 67, 67, 67, 67, 4, 4, 1, 1, 1, 76, 76, 92, 92, 92, 92, 92, 92, 92, 92, 92, 67, 67, 67, 67] 201 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 690 number of broken/clashed sets: 201 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517893 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C[N@H+]2CCCC(C(=O)[O-])C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 9, 6, 5, 5, 5, 5, 1, 11, 11, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 39, 67, 67, 67, 67, 9, 17, 17, 55, 77, 77, 77, 77, 77, 77, 104, 104, 77, 1, 1, 1, 2, 2, 2, 1, 1, 39, 39, 67, 67, 67, 55, 55, 77, 77, 77, 77, 77, 77, 77, 77, 77, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 49, 25, 26, 27, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50, 51, 52]) total number of confs: 576 number of broken/clashed sets: 201 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517893 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C[N@H+]2CCCC(C(=O)[O-])C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 9, 6, 5, 5, 5, 5, 1, 11, 11, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [59, 58, 77, 77, 30, 17, 30, 69, 92, 92, 92, 92, 5, 17, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 77, 77, 77, 77, 77, 77, 77, 77, 69, 69, 92, 92, 92, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 77, 77, 77, 77] 201 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 24, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 534 number of broken/clashed sets: 201 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517893 /scratch/stefan/7774842/working /scratch/stefan/7774842 mkdir: created directory `2' /scratch/stefan/7774842/working/building/REAL300004517893/2 /scratch/stefan/7774842/working/building/REAL300004517893 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 2 (index: 937) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/937 `/scratch/stefan/7774842/working/3D/937' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)CN2CCCC(C(=O)[O-])C2)C=C1C) `REAL300004517893.mol2' -> `2.mol2' `temp.mol2' -> `REAL300004517893.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517893/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517893 none CC1=CC=C(N(CC2=CC=CO2)C(=O)CN2CCCC(C(=O)[O-])C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 10, 5, 5, 5, 5, 1, 11, 11, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [47, 21, 81, 81, 21, 5, 1, 1, 1, 1, 1, 1, 21, 47, 47, 84, 92, 92, 92, 92, 92, 104, 104, 92, 81, 81, 81, 81, 81, 81, 81, 81, 5, 5, 1, 1, 1, 84, 84, 92, 92, 92, 92, 92, 92, 92, 92, 92, 81, 81, 81, 81] 201 rigid atoms, others: [34, 35, 36, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 757 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517893 none CC1=CC=C(N(CC2=CC=CO2)C(=O)CN2CCCC(C(=O)[O-])C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 10, 5, 5, 5, 5, 1, 11, 11, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 40, 81, 81, 81, 81, 11, 33, 33, 69, 83, 83, 83, 83, 83, 111, 111, 83, 1, 1, 1, 2, 2, 2, 1, 1, 40, 40, 81, 81, 81, 69, 69, 83, 83, 83, 83, 83, 83, 83, 83, 83, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 48, 24, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 49, 50, 51]) total number of confs: 565 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517893 none CC1=CC=C(N(CC2=CC=CO2)C(=O)CN2CCCC(C(=O)[O-])C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 10, 5, 5, 5, 5, 1, 11, 11, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [66, 32, 83, 83, 32, 18, 32, 69, 92, 92, 92, 92, 6, 18, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 83, 83, 83, 83, 83, 83, 83, 83, 69, 69, 92, 92, 92, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 83, 83, 83, 83] 201 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 46, 23, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 658 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517893 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517893 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 2: /scratch/stefan/7774842/working/building/REAL300004517893/2.* 1: /scratch/stefan/7774842/working/building/REAL300004517893/1.* 0: /scratch/stefan/7774842/working/building/REAL300004517893/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517893 Building REAL300004517894 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517894' /scratch/stefan/7774842/working/building/REAL300004517894 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517894 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517894/0 /scratch/stefan/7774842/working/building/REAL300004517894 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 938) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/938 `/scratch/stefan/7774842/working/3D/938' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@@H]2C[C@H]2C(=O)[O-])C=C1C) `REAL300004517894.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517894.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517894/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517894 none CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@@H]2C[C@H]2C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 7, 5, 5, 7, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [86, 86, 86, 86, 21, 5, 1, 1, 1, 1, 1, 1, 21, 57, 57, 87, 87, 87, 87, 87, 111, 111, 86, 86, 86, 86, 86, 86, 86, 86, 5, 5, 1, 1, 1, 87, 87, 86, 86, 86, 86] 201 rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40]) total number of confs: 429 number of broken/clashed sets: 13 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517894 none CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@@H]2C[C@H]2C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 7, 5, 5, 7, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 41, 86, 86, 86, 86, 11, 38, 38, 78, 78, 78, 78, 78, 102, 102, 1, 1, 1, 2, 2, 2, 1, 1, 41, 41, 86, 86, 86, 78, 78, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 22, 23, 24, 28, 29, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40]) total number of confs: 522 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517894 none CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@@H]2C[C@H]2C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 7, 5, 5, 7, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [78, 78, 78, 78, 27, 8, 27, 62, 87, 87, 87, 87, 1, 8, 1, 1, 1, 1, 1, 1, 3, 3, 78, 78, 78, 78, 78, 78, 78, 78, 62, 62, 87, 87, 87, 1, 1, 78, 78, 78, 78] 201 rigid atoms, others: [35, 36, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40]) total number of confs: 341 number of broken/clashed sets: 13 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517894 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517894 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517894/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517894 Building REAL300004517895 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517895' /scratch/stefan/7774842/working/building/REAL300004517895 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517895 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517895/0 /scratch/stefan/7774842/working/building/REAL300004517895 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 939) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/939 `/scratch/stefan/7774842/working/3D/939' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)C2CC3(CC3C(=O)[O-])C2)C=C1C) `REAL300004517895.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517895/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517895 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2CC3(CC3C(=O)[O-])C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 21, 79, 79, 21, 5, 1, 1, 1, 1, 1, 1, 21, 50, 50, 92, 92, 92, 92, 92, 112, 112, 92, 79, 79, 79, 79, 79, 79, 79, 79, 5, 5, 1, 1, 1, 92, 92, 92, 92, 92, 92, 92, 92, 79, 79, 79, 79] 201 rigid atoms, others: [33, 34, 35, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 728 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517895 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2CC3(CC3C(=O)[O-])C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 39, 79, 79, 79, 79, 11, 29, 29, 66, 66, 66, 66, 66, 101, 101, 66, 1, 1, 1, 2, 2, 2, 1, 1, 39, 39, 79, 79, 79, 66, 66, 66, 66, 66, 66, 66, 66, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 44, 23, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47]) total number of confs: 530 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517895 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2CC3(CC3C(=O)[O-])C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [45, 22, 66, 66, 22, 8, 22, 64, 92, 92, 92, 92, 1, 8, 1, 1, 1, 1, 1, 1, 3, 3, 1, 66, 66, 66, 66, 66, 66, 66, 66, 64, 64, 92, 92, 92, 1, 1, 1, 1, 1, 1, 1, 1, 66, 66, 66, 66] 201 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 44, 45, 46, 47]) total number of confs: 596 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517895 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517895 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517895/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517895 Building REAL300004517896 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517896' /scratch/stefan/7774842/working/building/REAL300004517896 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517896 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517896/0 /scratch/stefan/7774842/working/building/REAL300004517896 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 940) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/940 `/scratch/stefan/7774842/working/3D/940' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@H]2C[C@@H](C(=O)[O-])C2)C=C1C) `REAL300004517896.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517896 none CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@H]2C[C@@H](C(=O)[O-])C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 7, 5, 5, 7, 1, 11, 11, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 85, 85, 23, 5, 1, 1, 1, 1, 1, 1, 23, 47, 47, 103, 103, 103, 103, 103, 115, 115, 103, 85, 85, 85, 85, 85, 85, 85, 85, 5, 5, 1, 1, 1, 103, 103, 103, 103, 85, 85, 85, 85] 201 rigid atoms, others: [33, 34, 35, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 786 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517896 none CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@H]2C[C@@H](C(=O)[O-])C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 7, 5, 5, 7, 1, 11, 11, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 41, 85, 85, 85, 85, 11, 23, 23, 56, 56, 56, 56, 56, 88, 88, 56, 1, 1, 1, 2, 2, 2, 1, 1, 41, 41, 85, 85, 85, 56, 56, 56, 56, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 40, 23, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43]) total number of confs: 491 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517896 none CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@H]2C[C@@H](C(=O)[O-])C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 7, 5, 5, 7, 1, 11, 11, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 56, 56, 21, 8, 21, 72, 103, 103, 103, 103, 1, 8, 1, 1, 1, 1, 1, 1, 3, 3, 1, 56, 56, 56, 56, 56, 56, 56, 56, 72, 72, 103, 103, 103, 1, 1, 1, 1, 56, 56, 56, 56] 201 rigid atoms, others: [36, 37, 38, 39, 12, 14, 15, 16, 17, 18, 19, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 40, 41, 42, 43]) total number of confs: 612 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517896 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517896 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517896/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517896 Building REAL300004517897 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517897' /scratch/stefan/7774842/working/building/REAL300004517897 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517897 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517897/0 /scratch/stefan/7774842/working/building/REAL300004517897 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 941) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/941 `/scratch/stefan/7774842/working/3D/941' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@H]2C[C@]2(C(=O)[O-])C(C)C)C=C1C) `REAL300004517897.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517897/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517897 none CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@H]2C[C@]2(C(=O)[O-])C(C)C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 7, 5, 5, 1, 11, 11, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [34, 16, 53, 53, 16, 5, 1, 1, 1, 1, 1, 1, 16, 27, 27, 38, 38, 38, 38, 38, 38, 38, 45, 45, 53, 53, 53, 53, 53, 53, 53, 53, 4, 4, 1, 1, 1, 38, 38, 45, 45, 45, 45, 45, 45, 45, 53, 53, 53, 53] 84 rigid atoms, others: [34, 35, 36, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 405 number of broken/clashed sets: 14 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517897 none CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@H]2C[C@]2(C(=O)[O-])C(C)C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 7, 5, 5, 1, 11, 11, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 33, 53, 53, 53, 53, 11, 26, 26, 36, 36, 36, 36, 36, 36, 36, 56, 56, 1, 1, 1, 2, 2, 2, 1, 1, 33, 33, 53, 53, 53, 36, 36, 56, 56, 56, 56, 56, 56, 56, 1, 2, 2, 2] 84 rigid atoms, others: [0, 1, 2, 3, 4, 5, 46, 24, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49]) total number of confs: 361 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517897 none CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@H]2C[C@]2(C(=O)[O-])C(C)C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 7, 5, 5, 1, 11, 11, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 84 conformations in input total number of sets (complete confs): 84 using faster count positions algorithm for large data unique positions, atoms: [27, 14, 36, 36, 14, 6, 14, 26, 38, 38, 38, 38, 1, 6, 1, 1, 1, 1, 1, 2, 2, 1, 6, 6, 36, 36, 36, 36, 36, 36, 36, 36, 26, 26, 38, 38, 38, 1, 1, 6, 6, 6, 6, 6, 6, 6, 36, 36, 36, 36] 84 rigid atoms, others: [37, 38, 12, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 279 number of broken/clashed sets: 14 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517897 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517897 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517897/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517897 Building REAL300004517898 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517898' /scratch/stefan/7774842/working/building/REAL300004517898 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517898 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517898/0 /scratch/stefan/7774842/working/building/REAL300004517898 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 942) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/942 `/scratch/stefan/7774842/working/3D/942' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC(C(=O)[O-])=CC=C2C)C=C1C) `REAL300004517898.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517898/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517898 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC(C(=O)[O-])=CC=C2C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 52, 91, 91, 23, 5, 1, 1, 1, 1, 1, 1, 23, 66, 66, 100, 100, 100, 100, 100, 100, 100, 100, 100, 91, 91, 91, 91, 91, 91, 91, 91, 5, 5, 1, 1, 1, 100, 100, 100, 100, 100, 100, 91, 91, 91, 91] 201 rigid atoms, others: [34, 35, 36, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 585 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517898 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC(C(=O)[O-])=CC=C2C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 45, 91, 91, 91, 91, 11, 32, 32, 68, 68, 68, 68, 68, 68, 68, 68, 68, 1, 1, 1, 2, 2, 2, 1, 1, 45, 45, 91, 91, 91, 68, 68, 68, 68, 68, 68, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 43, 24, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46]) total number of confs: 366 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517898 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC(C(=O)[O-])=CC=C2C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 11, 11, 1, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [47, 47, 68, 68, 19, 7, 19, 65, 100, 100, 100, 100, 1, 7, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 68, 68, 68, 68, 68, 68, 68, 68, 65, 65, 100, 100, 100, 1, 1, 1, 2, 2, 2, 68, 68, 68, 68] 201 rigid atoms, others: [37, 38, 39, 12, 14, 15, 16, 17, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 18, 19, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 568 number of broken/clashed sets: 5 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517898 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517898 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517898/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517898 Building REAL300004517899 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517899' /scratch/stefan/7774842/working/building/REAL300004517899 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517899 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517899/0 /scratch/stefan/7774842/working/building/REAL300004517899 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 943) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/943 `/scratch/stefan/7774842/working/3D/943' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)C2CC(C)(C(=O)[O-])C2)C=C1C) `REAL300004517899.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517899.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517899/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517899 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2CC(C)(C(=O)[O-])C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 5, 5, 5, 1, 11, 11, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [42, 32, 66, 66, 19, 5, 1, 1, 1, 1, 1, 1, 19, 46, 46, 86, 86, 86, 86, 103, 103, 86, 66, 66, 66, 66, 66, 66, 66, 66, 5, 5, 1, 1, 1, 86, 86, 86, 86, 86, 86, 86, 86, 66, 66, 66, 66] 201 rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 596 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517899 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2CC(C)(C(=O)[O-])C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 5, 5, 5, 1, 11, 11, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 38, 66, 66, 66, 66, 11, 31, 31, 75, 75, 75, 75, 98, 98, 75, 1, 1, 1, 2, 2, 2, 1, 1, 38, 38, 66, 66, 66, 75, 75, 75, 75, 75, 75, 75, 75, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 43, 22, 23, 24, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46]) total number of confs: 478 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517899 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2CC(C)(C(=O)[O-])C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 5, 5, 5, 1, 11, 11, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 42, 75, 75, 24, 8, 24, 59, 86, 86, 86, 86, 1, 8, 1, 1, 1, 1, 1, 3, 3, 1, 75, 75, 75, 75, 75, 75, 75, 75, 59, 59, 86, 86, 86, 1, 1, 1, 2, 2, 2, 1, 1, 75, 75, 75, 75] 201 rigid atoms, others: [35, 36, 37, 41, 42, 12, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 43, 44, 45, 46]) total number of confs: 545 number of broken/clashed sets: 9 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517899 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517899 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517899/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517899 Building REAL300004517900 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517900' /scratch/stefan/7774842/working/building/REAL300004517900 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for REAL300004517900 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517900/0 /scratch/stefan/7774842/working/building/REAL300004517900 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 944) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/944 `/scratch/stefan/7774842/working/3D/944' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC(C(=O)[O-])=NN2)C=C1C) `REAL300004517900.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517900/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517900 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC(C(=O)[O-])=NN2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 11, 11, 8, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 55, 84, 84, 23, 4, 1, 1, 1, 1, 1, 1, 23, 61, 61, 107, 107, 107, 107, 107, 107, 107, 84, 84, 84, 84, 84, 84, 84, 84, 4, 4, 1, 1, 1, 107, 107, 84, 84, 84, 84] 201 rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40]) total number of confs: 567 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517900 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC(C(=O)[O-])=NN2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 11, 11, 8, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 41, 84, 84, 84, 84, 11, 27, 27, 70, 70, 70, 70, 70, 70, 70, 1, 1, 1, 2, 2, 2, 1, 1, 41, 41, 84, 84, 84, 70, 70, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 22, 23, 24, 28, 29, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40]) total number of confs: 337 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517900 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC(C(=O)[O-])=NN2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 11, 11, 8, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [58, 58, 70, 70, 27, 12, 27, 59, 107, 107, 107, 107, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 70, 70, 70, 70, 70, 70, 70, 70, 59, 59, 107, 107, 107, 1, 1, 70, 70, 70, 70] 201 rigid atoms, others: [35, 36, 12, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40]) total number of confs: 466 number of broken/clashed sets: 12 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517900 /scratch/stefan/7774842/working /scratch/stefan/7774842 mkdir: created directory `1' /scratch/stefan/7774842/working/building/REAL300004517900/1 /scratch/stefan/7774842/working/building/REAL300004517900 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 1 (index: 945) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/945 `/scratch/stefan/7774842/working/3D/945' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=NNC(C(=O)[O-])=C2)C=C1C) `REAL300004517900.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004517900.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517900/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517900 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=NNC(C(=O)[O-])=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 8, 8, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 23, 87, 87, 23, 5, 1, 1, 1, 1, 1, 1, 23, 60, 60, 108, 108, 108, 108, 108, 108, 108, 87, 87, 87, 87, 87, 87, 87, 87, 5, 5, 1, 1, 1, 108, 108, 87, 87, 87, 87] 201 rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40]) total number of confs: 698 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517900 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=NNC(C(=O)[O-])=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 8, 8, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 47, 87, 87, 87, 87, 11, 30, 30, 84, 84, 84, 84, 84, 84, 84, 1, 1, 1, 2, 2, 2, 1, 1, 47, 47, 87, 87, 87, 84, 84, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 22, 23, 24, 28, 29, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40]) total number of confs: 372 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517900 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=NNC(C(=O)[O-])=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 8, 8, 1, 1, 11, 11, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 84, 84, 35, 12, 35, 68, 108, 108, 108, 108, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 84, 84, 84, 84, 84, 84, 84, 84, 68, 68, 108, 108, 108, 1, 1, 84, 84, 84, 84] 201 rigid atoms, others: [35, 36, 12, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40]) total number of confs: 733 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517900 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517900 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 1: /scratch/stefan/7774842/working/building/REAL300004517900/1.* 0: /scratch/stefan/7774842/working/building/REAL300004517900/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517900 Building REAL300004517901 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517901' /scratch/stefan/7774842/working/building/REAL300004517901 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517901 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517901/0 /scratch/stefan/7774842/working/building/REAL300004517901 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 946) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/946 `/scratch/stefan/7774842/working/3D/946' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CN=CC(C(=O)[O-])=C2C)C=C1C) `REAL300004517901.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517901.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517901/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517901 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CN=CC(C(=O)[O-])=C2C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 8, 1, 1, 1, 11, 11, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [96, 96, 96, 96, 25, 5, 1, 1, 1, 1, 1, 1, 25, 66, 66, 98, 98, 98, 98, 98, 98, 98, 98, 98, 96, 96, 96, 96, 96, 96, 96, 96, 5, 5, 1, 1, 1, 98, 98, 98, 98, 98, 96, 96, 96, 96] 201 rigid atoms, others: [34, 35, 36, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 326 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517901 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CN=CC(C(=O)[O-])=C2C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 8, 1, 1, 1, 11, 11, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 45, 96, 96, 96, 96, 11, 42, 42, 81, 81, 81, 81, 81, 81, 81, 81, 81, 1, 1, 1, 2, 2, 2, 1, 1, 45, 45, 96, 96, 96, 81, 81, 81, 81, 81, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 42, 24, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 43, 44, 45]) total number of confs: 404 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517901 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CN=CC(C(=O)[O-])=C2C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 8, 1, 1, 1, 11, 11, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [81, 81, 81, 81, 23, 9, 23, 61, 98, 98, 98, 98, 1, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 81, 81, 81, 81, 81, 81, 81, 81, 61, 61, 98, 98, 98, 1, 1, 2, 2, 2, 81, 81, 81, 81] 201 rigid atoms, others: [37, 38, 12, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 386 number of broken/clashed sets: 9 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517901 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517901 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517901/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517901 Building REAL300004517902 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517902' /scratch/stefan/7774842/working/building/REAL300004517902 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517902 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517902/0 /scratch/stefan/7774842/working/building/REAL300004517902 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 947) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/947 `/scratch/stefan/7774842/working/3D/947' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(C(=O)[O-])C(=O)N(CC1=CC=CO1)C1=CC=C(C)C(C)=C1) `REAL300004517902.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517902.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517902/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517902 none CCCC(C(=O)[O-])C(=O)N(CC1=CC=CO1)C1=CC=C(C)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [78, 76, 36, 15, 36, 53, 53, 7, 15, 1, 7, 37, 66, 66, 66, 66, 1, 1, 1, 1, 1, 1, 1, 1, 78, 78, 78, 78, 78, 76, 76, 36, 37, 37, 66, 66, 66, 1, 1, 2, 2, 2, 2, 2, 2, 1] 201 rigid atoms, others: [37, 38, 9, 45, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 14, 15, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44]) total number of confs: 574 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517902 none CCCC(C(=O)[O-])C(=O)N(CC1=CC=CO1)C1=CC=C(C)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 11, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 2, 2, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [113, 112, 69, 34, 69, 89, 89, 19, 34, 4, 1, 1, 1, 1, 1, 1, 19, 66, 66, 19, 19, 66, 66, 66, 113, 113, 113, 113, 113, 112, 112, 69, 4, 4, 1, 1, 1, 66, 66, 66, 66, 66, 66, 66, 66, 66] 201 rigid atoms, others: [34, 35, 36, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 932 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517902 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517902 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517902/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517902 Building REAL300004517903 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517903' /scratch/stefan/7774842/working/building/REAL300004517903 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517903 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517903/0 /scratch/stefan/7774842/working/building/REAL300004517903 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 948) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/948 `/scratch/stefan/7774842/working/3D/948' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(C(=O)[O-])C=C2C)C=C1C) `REAL300004517903.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517903.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517903/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517903 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(C(=O)[O-])C=C2C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 90, 90, 90, 23, 5, 1, 1, 1, 1, 1, 1, 23, 63, 63, 96, 96, 89, 89, 96, 96, 96, 96, 96, 90, 90, 90, 90, 90, 90, 90, 90, 5, 5, 1, 1, 1, 96, 96, 96, 96, 96, 96, 90, 90, 90, 90] 201 rigid atoms, others: [34, 35, 36, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 371 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517903 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(C(=O)[O-])C=C2C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 44, 90, 90, 90, 90, 11, 38, 38, 77, 77, 67, 68, 77, 77, 77, 77, 77, 1, 1, 1, 2, 2, 2, 1, 1, 44, 44, 90, 90, 90, 77, 77, 77, 77, 77, 77, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 43, 24, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46]) total number of confs: 448 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517903 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(C(=O)[O-])C=C2C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 77, 77, 22, 9, 22, 66, 96, 96, 96, 96, 1, 9, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 77, 77, 77, 77, 77, 77, 77, 77, 66, 66, 96, 96, 96, 1, 1, 1, 2, 2, 2, 77, 77, 77, 77] 201 rigid atoms, others: [37, 38, 39, 12, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 376 number of broken/clashed sets: 5 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517903 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517903 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517903/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517903 Building REAL300004517904 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517904' /scratch/stefan/7774842/working/building/REAL300004517904 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517904 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517904/0 /scratch/stefan/7774842/working/building/REAL300004517904 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 949) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/949 `/scratch/stefan/7774842/working/3D/949' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(C(=O)[O-])C=C2Cl)C=C1C) `REAL300004517904.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517904.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517904/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517904 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(C(=O)[O-])C=C2Cl)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [50, 25, 92, 92, 25, 5, 1, 1, 1, 1, 1, 1, 25, 70, 70, 106, 106, 96, 106, 106, 106, 106, 106, 106, 92, 92, 92, 92, 92, 92, 92, 92, 5, 5, 1, 1, 1, 106, 106, 106, 92, 92, 92, 92] 201 rigid atoms, others: [34, 35, 36, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 731 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517904 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(C(=O)[O-])C=C2Cl)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 45, 92, 92, 92, 92, 11, 35, 35, 76, 76, 64, 76, 76, 76, 76, 76, 76, 1, 1, 1, 2, 2, 2, 1, 1, 45, 45, 92, 92, 92, 76, 76, 76, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 40, 24, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43]) total number of confs: 447 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517904 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(C(=O)[O-])C=C2Cl)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'Cl', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 16, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [52, 23, 76, 76, 23, 7, 23, 69, 106, 106, 106, 106, 1, 7, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 76, 76, 76, 76, 76, 76, 76, 76, 69, 69, 106, 106, 106, 1, 1, 1, 76, 76, 76, 76] 201 rigid atoms, others: [37, 38, 39, 12, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43]) total number of confs: 675 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517904 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517904 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517904/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517904 Building REAL300004517905 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517905' /scratch/stefan/7774842/working/building/REAL300004517905 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517905 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517905/0 /scratch/stefan/7774842/working/building/REAL300004517905 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 950) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/950 `/scratch/stefan/7774842/working/3D/950' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)C2CC3(CC(C(=O)[O-])C3)C2)C=C1C) `REAL300004517905.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517905/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517905 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2CC3(CC(C(=O)[O-])C3)C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 30, 82, 82, 19, 4, 1, 1, 1, 1, 1, 1, 19, 41, 41, 89, 89, 89, 89, 89, 116, 116, 89, 89, 82, 82, 82, 80, 81, 81, 82, 82, 4, 4, 1, 1, 1, 89, 89, 89, 89, 89, 89, 89, 89, 89, 89, 82, 82, 82, 82] 201 rigid atoms, others: [34, 35, 36, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 798 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517905 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2CC3(CC(C(=O)[O-])C3)C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 43, 82, 82, 82, 82, 11, 27, 27, 55, 55, 55, 55, 55, 86, 86, 55, 55, 1, 1, 1, 2, 2, 2, 1, 1, 43, 43, 82, 82, 82, 55, 55, 55, 55, 55, 55, 55, 55, 55, 55, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 47, 24, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 48, 49, 50]) total number of confs: 500 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517905 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2CC3(CC(C(=O)[O-])C3)C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 36, 55, 55, 19, 8, 19, 54, 89, 89, 89, 89, 1, 8, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 55, 55, 55, 55, 55, 55, 55, 55, 54, 54, 89, 89, 89, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 55, 55, 55, 55] 201 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 46, 22, 23, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 47, 48, 49, 50]) total number of confs: 546 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517905 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517905 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517905/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517905 Building REAL300004517906 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517906' /scratch/stefan/7774842/working/building/REAL300004517906 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517906 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517906/0 /scratch/stefan/7774842/working/building/REAL300004517906 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 951) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/951 `/scratch/stefan/7774842/working/3D/951' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC1=CC(C(=O)[O-])=NC(C(=O)N(CC2=CC=CO2)C2=CC=C(C)C(C)=C2)=C1) `REAL300004517906.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517906.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517906/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517906 none COC1=CC(C(=O)[O-])=NC(C(=O)N(CC2=CC=CO2)C2=CC=C(C)C(C)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 93, 93, 93, 93, 93, 93, 93, 93, 55, 23, 55, 4, 1, 1, 1, 1, 1, 1, 23, 83, 83, 45, 53, 83, 83, 83, 93, 101, 101, 101, 93, 4, 4, 1, 1, 1, 83, 83, 83, 83, 83, 83, 83, 83, 83, 93] 201 rigid atoms, others: [34, 35, 36, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 573 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517906 none COC1=CC(C(=O)[O-])=NC(C(=O)N(CC2=CC=CO2)C2=CC=C(C)C(C)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [3, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 8, 8, 23, 61, 93, 93, 93, 93, 23, 73, 73, 51, 59, 73, 73, 73, 1, 3, 3, 3, 1, 61, 61, 93, 93, 93, 73, 73, 73, 73, 73, 73, 73, 73, 73, 1] 201 rigid atoms, others: [1, 2, 3, 4, 5, 8, 9, 10, 46, 27, 31] set([0, 6, 7, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 28, 29, 30, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 518 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517906 none COC1=CC(C(=O)[O-])=NC(C(=O)N(CC2=CC=CO2)C2=CC=C(C)C(C)=C2)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 11, 8, 1, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 1, 5, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 2, 2, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [91, 73, 73, 73, 73, 73, 73, 73, 73, 35, 11, 35, 1, 11, 45, 83, 83, 83, 83, 1, 1, 1, 1, 1, 1, 1, 1, 73, 91, 91, 91, 73, 45, 45, 83, 83, 83, 1, 1, 2, 2, 2, 2, 2, 2, 1, 73] 201 rigid atoms, others: [37, 38, 12, 45, 19, 20, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 15, 16, 17, 18, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 39, 40, 41, 42, 43, 44, 46]) total number of confs: 388 number of broken/clashed sets: 9 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517906 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517906 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517906/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517906 Building REAL300004517907 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517907' /scratch/stefan/7774842/working/building/REAL300004517907 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517907 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517907/0 /scratch/stefan/7774842/working/building/REAL300004517907 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 952) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/952 `/scratch/stefan/7774842/working/3D/952' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(C(=O)[O-])N2C)C=C1C) `REAL300004517907.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517907.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517907/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517907 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(C(=O)[O-])N2C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 11, 11, 8, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [90, 90, 90, 90, 23, 5, 1, 1, 1, 1, 1, 1, 23, 64, 64, 101, 101, 101, 101, 101, 101, 101, 101, 90, 90, 90, 90, 90, 90, 90, 90, 5, 5, 1, 1, 1, 101, 101, 101, 101, 101, 90, 90, 90, 90] 201 rigid atoms, others: [33, 34, 35, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 322 number of broken/clashed sets: 7 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517907 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(C(=O)[O-])N2C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 11, 11, 8, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 45, 90, 90, 90, 90, 11, 34, 34, 77, 77, 77, 77, 77, 77, 77, 77, 1, 1, 1, 2, 2, 2, 1, 1, 45, 45, 90, 90, 90, 77, 77, 77, 77, 77, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 41, 23, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44]) total number of confs: 376 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517907 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(C(=O)[O-])N2C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 11, 11, 8, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [77, 77, 77, 77, 25, 9, 25, 61, 101, 101, 101, 101, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 77, 77, 77, 77, 77, 77, 77, 77, 61, 61, 101, 101, 101, 1, 1, 2, 2, 2, 77, 77, 77, 77] 201 rigid atoms, others: [36, 37, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 373 number of broken/clashed sets: 7 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517907 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517907 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517907/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517907 Building REAL300004517908 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517908' /scratch/stefan/7774842/working/building/REAL300004517908 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517908 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517908/0 /scratch/stefan/7774842/working/building/REAL300004517908 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 953) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/953 `/scratch/stefan/7774842/working/3D/953' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(CCC(=O)[O-])C=C2)C=C1C) `REAL300004517908.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517908.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517908/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517908 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(CCC(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 5, 5, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 17, 62, 62, 17, 4, 1, 1, 1, 1, 1, 1, 17, 39, 39, 54, 54, 45, 45, 93, 110, 124, 124, 54, 54, 62, 62, 62, 60, 62, 62, 62, 62, 4, 4, 1, 1, 1, 54, 54, 93, 93, 110, 110, 54, 54, 62, 62, 62, 62] 201 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 885 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517908 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(CCC(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 5, 5, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 30, 62, 62, 62, 62, 11, 27, 27, 32, 32, 29, 29, 54, 76, 108, 108, 32, 32, 1, 1, 1, 2, 2, 2, 1, 1, 30, 30, 62, 62, 62, 32, 32, 54, 54, 76, 76, 32, 32, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 46, 25, 26, 27, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49]) total number of confs: 606 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517908 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=C(CCC(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 5, 5, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [14, 14, 32, 32, 14, 6, 14, 30, 54, 54, 54, 54, 1, 6, 1, 1, 1, 1, 1, 2, 6, 11, 11, 1, 1, 32, 32, 32, 32, 32, 32, 32, 32, 30, 30, 54, 54, 54, 1, 1, 2, 2, 6, 6, 1, 1, 32, 32, 32, 32] 201 rigid atoms, others: [38, 39, 44, 12, 45, 14, 15, 16, 17, 18, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43, 46, 47, 48, 49]) total number of confs: 352 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517908 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517908 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517908/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517908 Building REAL300004517909 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517909' /scratch/stefan/7774842/working/building/REAL300004517909 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517909 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517909/0 /scratch/stefan/7774842/working/building/REAL300004517909 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 954) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/954 `/scratch/stefan/7774842/working/3D/954' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)CC2(CC(=O)[O-])CC2)C=C1C) `REAL300004517909.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517909.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517909/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517909 none CC1=CC=C(N(CC2=CC=CO2)C(=O)CC2(CC(=O)[O-])CC2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 5, 5, 1, 11, 11, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [44, 22, 87, 87, 22, 5, 1, 1, 1, 1, 1, 1, 22, 44, 44, 90, 110, 130, 134, 134, 110, 110, 87, 87, 87, 87, 87, 87, 87, 87, 5, 5, 1, 1, 1, 90, 90, 130, 130, 110, 110, 110, 110, 87, 87, 87, 87] 201 rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 1002 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517909 none CC1=CC=C(N(CC2=CC=CO2)C(=O)CC2(CC(=O)[O-])CC2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 5, 5, 1, 11, 11, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 48, 87, 87, 87, 87, 11, 25, 25, 61, 84, 112, 130, 130, 84, 84, 1, 1, 1, 2, 2, 2, 1, 1, 48, 48, 87, 87, 87, 61, 61, 112, 112, 84, 84, 84, 84, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 43, 22, 23, 24, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46]) total number of confs: 779 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517909 none CC1=CC=C(N(CC2=CC=CO2)C(=O)CC2(CC(=O)[O-])CC2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 5, 5, 1, 11, 11, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [62, 33, 84, 84, 32, 14, 33, 78, 110, 110, 110, 110, 5, 14, 1, 1, 1, 6, 12, 12, 1, 1, 84, 84, 84, 84, 84, 84, 84, 84, 78, 78, 110, 110, 110, 5, 5, 6, 6, 1, 1, 1, 1, 84, 84, 84, 84] 201 rigid atoms, others: [39, 40, 41, 42, 14, 15, 16, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 17, 18, 19, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 43, 44, 45, 46]) total number of confs: 753 number of broken/clashed sets: 16 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517909 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517909 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517909/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517909 Building REAL300004517910 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517910' /scratch/stefan/7774842/working/building/REAL300004517910 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517910 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517910/0 /scratch/stefan/7774842/working/building/REAL300004517910 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 955) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/955 `/scratch/stefan/7774842/working/3D/955' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)C2CC3(C2)C(C(=O)[O-])C3(F)F)C=C1C) `REAL300004517910.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517910.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517910/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517910 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2CC3(C2)C(C(=O)[O-])C3(F)F)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 20, 76, 76, 19, 4, 1, 1, 1, 1, 1, 1, 19, 49, 49, 98, 98, 98, 98, 98, 114, 114, 98, 98, 98, 76, 76, 76, 76, 76, 75, 76, 76, 4, 4, 1, 1, 1, 98, 98, 98, 98, 98, 98, 76, 76, 76, 76] 201 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 735 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517910 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2CC3(C2)C(C(=O)[O-])C3(F)F)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 41, 76, 76, 76, 76, 11, 34, 34, 84, 84, 84, 84, 84, 111, 111, 84, 84, 84, 1, 1, 1, 2, 2, 2, 1, 1, 41, 41, 76, 76, 76, 84, 84, 84, 84, 84, 84, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 44, 25, 26, 27, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47]) total number of confs: 541 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517910 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2CC3(C2)C(C(=O)[O-])C3(F)F)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'F', 'F', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 15, 15, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [24, 24, 84, 84, 24, 8, 24, 72, 98, 98, 98, 98, 1, 8, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 84, 84, 84, 84, 84, 84, 84, 84, 72, 72, 98, 98, 98, 1, 1, 1, 1, 1, 1, 84, 84, 84, 84] 201 rigid atoms, others: [38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 44, 45, 46, 47]) total number of confs: 755 number of broken/clashed sets: 5 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517910 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517910 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517910/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517910 Building REAL300004517911 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517911' /scratch/stefan/7774842/working/building/REAL300004517911 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517911 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517911/0 /scratch/stefan/7774842/working/building/REAL300004517911 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 956) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/956 `/scratch/stefan/7774842/working/3D/956' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CSC(C(=O)[O-])=N2)C=C1C) `REAL300004517911.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517911.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517911/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517911 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CSC(C(=O)[O-])=N2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 14, 1, 1, 11, 11, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [98, 56, 98, 98, 22, 5, 1, 1, 1, 1, 1, 1, 22, 63, 63, 99, 99, 99, 99, 99, 99, 99, 98, 98, 98, 98, 98, 98, 98, 98, 5, 5, 1, 1, 1, 99, 98, 98, 98, 98] 201 rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39]) total number of confs: 512 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517911 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CSC(C(=O)[O-])=N2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 14, 1, 1, 11, 11, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 46, 98, 98, 98, 98, 11, 37, 37, 94, 94, 94, 94, 94, 94, 94, 1, 1, 1, 2, 2, 2, 1, 1, 46, 46, 98, 98, 98, 94, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 22, 23, 24, 36, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 30, 31, 32, 33, 34, 35, 37, 38, 39]) total number of confs: 417 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517911 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CSC(C(=O)[O-])=N2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'S.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 14, 1, 1, 11, 11, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [94, 66, 94, 94, 26, 10, 26, 66, 99, 99, 99, 99, 1, 10, 1, 1, 1, 1, 1, 2, 2, 1, 94, 94, 94, 94, 94, 94, 94, 94, 66, 66, 99, 99, 99, 1, 94, 94, 94, 94] 201 rigid atoms, others: [35, 12, 14, 15, 16, 17, 18, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39]) total number of confs: 531 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517911 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517911 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517911/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517911 Building REAL300004517912 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517912' /scratch/stefan/7774842/working/building/REAL300004517912 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517912 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517912/0 /scratch/stefan/7774842/working/building/REAL300004517912 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 957) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/957 `/scratch/stefan/7774842/working/3D/957' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(C(=O)[O-])C(=O)N(CC1=CC=CO1)C1=CC=C(C)C(C)=C1) `REAL300004517912.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517912/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517912 none COC(C(=O)[O-])C(=O)N(CC1=CC=CO1)C1=CC=C(C)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 11, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 2, 2, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [80, 50, 24, 50, 69, 69, 11, 24, 1, 11, 43, 98, 98, 98, 98, 1, 1, 1, 1, 1, 1, 1, 1, 80, 80, 80, 50, 43, 43, 98, 98, 98, 1, 1, 2, 2, 2, 2, 2, 2, 1] 201 rigid atoms, others: [32, 33, 8, 15, 16, 17, 18, 19, 20, 21, 22, 40] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 34, 35, 36, 37, 38, 39]) total number of confs: 536 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517912 none COC(C(=O)[O-])C(=O)N(CC1=CC=CO1)C1=CC=C(C)C(C)=C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 11, 11, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 1, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 2, 2, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [114, 102, 54, 102, 110, 110, 24, 54, 5, 1, 1, 1, 1, 1, 1, 24, 98, 98, 24, 24, 98, 98, 98, 114, 114, 114, 102, 5, 5, 1, 1, 1, 98, 98, 98, 98, 98, 98, 98, 98, 98] 201 rigid atoms, others: [9, 10, 11, 12, 13, 14, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 939 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517912 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517912 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517912/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517912 Building REAL300004517913 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517913' /scratch/stefan/7774842/working/building/REAL300004517913 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517913 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517913/0 /scratch/stefan/7774842/working/building/REAL300004517913 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 958) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/958 `/scratch/stefan/7774842/working/3D/958' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@@]2(C)C[C@H]2C(=O)[O-])C=C1C) `REAL300004517913.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517913.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517913/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517913 none CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@@]2(C)C[C@H]2C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 5, 5, 5, 7, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [14, 14, 30, 30, 14, 5, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 16, 16, 30, 30, 30, 30, 30, 30, 30, 30, 5, 5, 1, 1, 1, 14, 14, 14, 14, 14, 30, 30, 30, 30] 30 rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 200 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517913 none CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@@]2(C)C[C@H]2C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 5, 5, 5, 7, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 7, 19, 30, 30, 30, 30, 7, 11, 11, 11, 11, 11, 11, 11, 13, 13, 1, 1, 1, 2, 2, 2, 1, 1, 19, 19, 30, 30, 30, 11, 11, 11, 11, 11, 1, 2, 2, 2] 30 rigid atoms, others: [0, 1, 2, 3, 4, 5, 40, 22, 23, 24, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43]) total number of confs: 127 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517913 none CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@@]2(C)C[C@H]2C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 5, 5, 5, 7, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 30 conformations in input total number of sets (complete confs): 30 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 11, 11, 4, 2, 4, 9, 14, 14, 14, 14, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 11, 11, 11, 11, 11, 11, 11, 11, 9, 9, 14, 14, 14, 2, 2, 2, 1, 1, 11, 11, 11, 11] 30 rigid atoms, others: [38, 39, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 106 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517913 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517913 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517913/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517913 Building REAL300004517914 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517914' /scratch/stefan/7774842/working/building/REAL300004517914 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517914 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517914/0 /scratch/stefan/7774842/working/building/REAL300004517914 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 959) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/959 `/scratch/stefan/7774842/working/3D/959' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=C(C(=O)N(CC2=CC=CO2)C2=CC=C(C)C(C)=C2)C=C(C(=O)[O-])S1) `REAL300004517914.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517914.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517914/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517914 none CC1=C(C(=O)N(CC2=CC=CO2)C2=CC=C(C)C(C)=C2)C=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 1, 5, 1, 1, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [105, 105, 65, 23, 65, 5, 1, 1, 1, 1, 1, 1, 23, 82, 82, 29, 23, 82, 82, 82, 105, 105, 105, 105, 105, 105, 105, 105, 105, 5, 5, 1, 1, 1, 82, 82, 82, 82, 82, 82, 82, 82, 82, 105] 201 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 657 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517914 none CC1=C(C(=O)N(CC2=CC=CO2)C2=CC=C(C)C(C)=C2)C=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 1, 5, 1, 1, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 7, 7, 25, 65, 105, 105, 105, 105, 25, 70, 70, 33, 25, 70, 70, 70, 1, 1, 1, 2, 2, 1, 2, 2, 2, 65, 65, 105, 105, 105, 70, 70, 70, 70, 70, 70, 70, 70, 70, 1] 201 rigid atoms, others: [0, 1, 2, 3, 43, 20, 21, 22, 25] set([4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 23, 24, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 664 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517914 none CC1=C(C(=O)N(CC2=CC=CO2)C2=CC=C(C)C(C)=C2)C=C(C(=O)[O-])S1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.3', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 1, 1, 1, 1, 12, 1, 1, 1, 1, 5, 1, 5, 1, 1, 1, 1, 11, 11, 14, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [70, 70, 36, 11, 36, 1, 11, 33, 82, 82, 82, 82, 1, 1, 1, 1, 1, 1, 1, 1, 70, 70, 70, 70, 70, 70, 70, 70, 70, 33, 33, 82, 82, 82, 1, 1, 2, 2, 2, 2, 2, 2, 1, 70] 201 rigid atoms, others: [34, 35, 5, 42, 12, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 6, 7, 8, 9, 10, 11, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39, 40, 41, 43]) total number of confs: 336 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517914 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517914 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517914/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517914 Building REAL300004517915 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517915' /scratch/stefan/7774842/working/building/REAL300004517915 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517915 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517915/0 /scratch/stefan/7774842/working/building/REAL300004517915 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 960) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/960 `/scratch/stefan/7774842/working/3D/960' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)CCC2=CC=CN=C2C(=O)[O-])C=C1C) `REAL300004517915.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517915 none CC1=CC=C(N(CC2=CC=CO2)C(=O)CCC2=CC=CN=C2C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 5, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [11, 11, 27, 27, 11, 3, 1, 1, 1, 1, 1, 1, 11, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 27, 27, 27, 27, 27, 27, 27, 27, 3, 3, 1, 1, 1, 17, 17, 17, 17, 17, 17, 17, 27, 27, 27, 27] 27 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 172 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517915 none CC1=CC=C(N(CC2=CC=CO2)C(=O)CCC2=CC=CN=C2C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 5, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 9, 19, 27, 27, 27, 27, 9, 9, 9, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 1, 1, 1, 2, 2, 2, 1, 1, 19, 19, 27, 27, 27, 11, 11, 11, 11, 11, 11, 11, 1, 2, 2, 2] 27 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 45, 25, 26, 27, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48]) total number of confs: 107 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517915 none CC1=CC=C(N(CC2=CC=CO2)C(=O)CCC2=CC=CN=C2C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 5, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 27 conformations in input total number of sets (complete confs): 27 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 11, 11, 5, 3, 5, 9, 17, 17, 17, 17, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 11, 11, 11, 11, 11, 11, 11, 11, 9, 9, 17, 17, 17, 3, 3, 3, 3, 1, 1, 1, 11, 11, 11, 11] 27 rigid atoms, others: [42, 43, 44, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 45, 46, 47, 48]) total number of confs: 114 number of broken/clashed sets: 11 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517915 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517915 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517915/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517915 Building REAL300004517916 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517916' /scratch/stefan/7774842/working/building/REAL300004517916 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517916 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517916/0 /scratch/stefan/7774842/working/building/REAL300004517916 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 961) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/961 `/scratch/stefan/7774842/working/3D/961' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)C(C)C(=O)[O-])C=C1C) `REAL300004517916.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517916.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517916/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517916 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C(C)C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 5, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 180 conformations in input total number of sets (complete confs): 180 using faster count positions algorithm for large data unique positions, atoms: [25, 25, 106, 106, 25, 5, 1, 1, 1, 1, 1, 1, 25, 63, 63, 95, 95, 103, 103, 106, 106, 106, 106, 106, 104, 106, 106, 5, 5, 1, 1, 1, 95, 95, 95, 95, 106, 106, 106, 106] 180 rigid atoms, others: [6, 7, 8, 9, 10, 11, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 914 number of broken/clashed sets: 22 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517916 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C(C)C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 5, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 180 conformations in input total number of sets (complete confs): 180 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 48, 106, 106, 106, 106, 11, 32, 32, 59, 59, 75, 75, 1, 1, 1, 2, 2, 2, 1, 1, 48, 48, 106, 106, 106, 59, 59, 59, 59, 1, 2, 2, 2] 180 rigid atoms, others: [0, 1, 2, 3, 4, 5, 19, 20, 21, 25, 26, 36] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39]) total number of confs: 527 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517916 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517916 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517916/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517916 Building REAL300004517917 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517917' /scratch/stefan/7774842/working/building/REAL300004517917 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517917 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517917/0 /scratch/stefan/7774842/working/building/REAL300004517917 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 962) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/962 `/scratch/stefan/7774842/working/3D/962' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)/C=C/C2=CC=C(C(=O)[O-])C=C2)C=C1C) `REAL300004517917.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517917/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517917 none CC1=CC=C(N(CC2=CC=CO2)C(=O)/C=C/C2=CC=C(C(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [74, 46, 74, 74, 20, 5, 1, 1, 1, 1, 1, 1, 20, 43, 43, 102, 102, 115, 115, 102, 102, 115, 115, 115, 115, 74, 74, 74, 74, 74, 74, 74, 74, 5, 5, 1, 1, 1, 109, 109, 115, 115, 115, 115, 74, 74, 74, 74] 201 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 613 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517917 none CC1=CC=C(N(CC2=CC=CO2)C(=O)/C=C/C2=CC=C(C(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 37, 74, 74, 74, 74, 11, 27, 27, 84, 84, 106, 106, 84, 84, 106, 106, 106, 106, 1, 1, 1, 2, 2, 2, 1, 1, 37, 37, 74, 74, 74, 84, 84, 106, 106, 106, 106, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 44, 25, 26, 27, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 45, 46, 47]) total number of confs: 600 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517917 none CC1=CC=C(N(CC2=CC=CO2)C(=O)/C=C/C2=CC=C(C(=O)[O-])C=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [106, 82, 106, 106, 44, 18, 44, 92, 115, 115, 115, 115, 3, 18, 3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 106, 106, 106, 106, 106, 106, 106, 106, 92, 92, 115, 115, 115, 3, 3, 1, 1, 1, 1, 106, 106, 106, 106] 201 rigid atoms, others: [40, 41, 42, 43, 15, 16, 17, 18, 19, 20, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 44, 45, 46, 47]) total number of confs: 600 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517917 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517917 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517917/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517917 Building REAL300004517918 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517918' /scratch/stefan/7774842/working/building/REAL300004517918 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517918 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517918/0 /scratch/stefan/7774842/working/building/REAL300004517918 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 963) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/963 `/scratch/stefan/7774842/working/3D/963' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC3=C(N2)C(C(=O)[O-])=CS3)C=C1C) `REAL300004517918.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517918 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC3=C(N2)C(C(=O)[O-])=CS3)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 14, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 21, 84, 84, 21, 4, 1, 1, 1, 1, 1, 1, 21, 52, 52, 106, 106, 106, 106, 106, 106, 106, 106, 106, 106, 84, 84, 84, 84, 84, 84, 84, 84, 4, 4, 1, 1, 1, 106, 106, 106, 84, 84, 84, 84] 201 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 652 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517918 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC3=C(N2)C(C(=O)[O-])=CS3)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 14, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 41, 84, 84, 84, 84, 11, 33, 33, 91, 91, 91, 91, 91, 91, 91, 91, 91, 91, 1, 1, 1, 2, 2, 2, 1, 1, 41, 41, 84, 84, 84, 91, 91, 91, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 41, 25, 26, 27, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44]) total number of confs: 377 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517918 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC3=C(N2)C(C(=O)[O-])=CS3)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 14, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [32, 32, 91, 91, 32, 12, 32, 80, 106, 106, 106, 106, 1, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 91, 91, 91, 91, 91, 91, 91, 91, 80, 80, 106, 106, 106, 1, 1, 1, 91, 91, 91, 91] 201 rigid atoms, others: [38, 39, 40, 12, 14, 15, 16, 17, 18, 19, 20, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44]) total number of confs: 809 number of broken/clashed sets: 8 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517918 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517918 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517918/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517918 Building REAL300004517919 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517919' /scratch/stefan/7774842/working/building/REAL300004517919 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517919 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517919/0 /scratch/stefan/7774842/working/building/REAL300004517919 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 964) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/964 `/scratch/stefan/7774842/working/3D/964' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC3=C(C=C(C(=O)[O-])S3)N2)C=C1C) `REAL300004517919.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517919.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517919/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517919 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC3=C(C=C(C(=O)[O-])S3)N2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'N.pl3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 14, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [57, 49, 89, 89, 25, 5, 1, 1, 1, 1, 1, 1, 25, 54, 54, 104, 104, 104, 104, 104, 104, 104, 104, 104, 104, 89, 89, 89, 89, 89, 89, 89, 89, 5, 5, 1, 1, 1, 104, 104, 104, 89, 89, 89, 89] 201 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 600 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517919 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC3=C(C=C(C(=O)[O-])S3)N2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'N.pl3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 14, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 45, 89, 89, 89, 89, 11, 37, 37, 96, 96, 96, 96, 96, 96, 96, 96, 96, 96, 1, 1, 1, 2, 2, 2, 1, 1, 45, 45, 89, 89, 89, 96, 96, 96, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 41, 25, 26, 27, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44]) total number of confs: 401 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517919 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC3=C(C=C(C(=O)[O-])S3)N2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'N.pl3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 14, 8, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [80, 80, 96, 96, 38, 12, 38, 76, 104, 104, 104, 104, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 96, 96, 96, 96, 96, 96, 96, 96, 76, 76, 104, 104, 104, 1, 1, 1, 96, 96, 96, 96] 201 rigid atoms, others: [38, 39, 40, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44]) total number of confs: 554 number of broken/clashed sets: 16 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517919 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517919 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517919/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517919 Building REAL300004517920 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517920' /scratch/stefan/7774842/working/building/REAL300004517920 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517920 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517920/0 /scratch/stefan/7774842/working/building/REAL300004517920 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 965) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/965 `/scratch/stefan/7774842/working/3D/965' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC3=C(N2)C(C(=O)[O-])=CO3)C=C1C) `REAL300004517920.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517920/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517920 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC3=C(N2)C(C(=O)[O-])=CO3)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [37, 20, 81, 81, 20, 5, 1, 1, 1, 1, 1, 1, 20, 46, 46, 107, 107, 107, 107, 107, 107, 107, 107, 107, 107, 81, 81, 81, 81, 81, 81, 81, 81, 5, 5, 1, 1, 1, 107, 107, 107, 81, 81, 81, 81] 201 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 621 number of broken/clashed sets: 9 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517920 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC3=C(N2)C(C(=O)[O-])=CO3)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 41, 81, 81, 81, 81, 11, 33, 33, 92, 92, 92, 92, 92, 92, 92, 92, 92, 92, 1, 1, 1, 2, 2, 2, 1, 1, 41, 41, 81, 81, 81, 92, 92, 92, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 41, 25, 26, 27, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 42, 43, 44]) total number of confs: 372 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517920 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC3=C(N2)C(C(=O)[O-])=CO3)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 8, 1, 1, 11, 11, 1, 12, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 4, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [68, 31, 92, 92, 31, 12, 31, 82, 107, 107, 107, 107, 1, 12, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 92, 92, 92, 92, 92, 92, 92, 92, 82, 82, 107, 107, 107, 1, 1, 1, 92, 92, 92, 92] 201 rigid atoms, others: [38, 39, 40, 12, 14, 15, 16, 17, 18, 19, 20, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 21, 22, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44]) total number of confs: 774 number of broken/clashed sets: 9 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517920 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517920 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517920/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517920 Building REAL300004517921 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517921' /scratch/stefan/7774842/working/building/REAL300004517921 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517921 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517921/0 /scratch/stefan/7774842/working/building/REAL300004517921 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 966) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/966 `/scratch/stefan/7774842/working/3D/966' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=CC(C(=O)[O-])=C2C)C=C1C) `REAL300004517921.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517921.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517921/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517921 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=CC(C(=O)[O-])=C2C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [62, 52, 94, 94, 25, 5, 1, 1, 1, 1, 1, 1, 25, 73, 73, 101, 101, 101, 101, 101, 101, 101, 101, 101, 94, 94, 94, 94, 94, 94, 94, 94, 5, 5, 1, 1, 1, 101, 101, 101, 101, 101, 101, 94, 94, 94, 94] 201 rigid atoms, others: [34, 35, 36, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 604 number of broken/clashed sets: 8 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517921 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=CC(C(=O)[O-])=C2C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 48, 94, 94, 94, 94, 11, 41, 41, 88, 88, 88, 88, 88, 88, 88, 88, 88, 1, 1, 1, 2, 2, 2, 1, 1, 48, 48, 94, 94, 94, 88, 88, 88, 88, 88, 88, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 43, 24, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46]) total number of confs: 414 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517921 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=CC(C(=O)[O-])=C2C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [56, 49, 88, 88, 23, 9, 23, 66, 101, 101, 101, 101, 1, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 88, 88, 88, 88, 88, 88, 88, 88, 66, 66, 101, 101, 101, 1, 1, 1, 2, 2, 2, 88, 88, 88, 88] 201 rigid atoms, others: [37, 38, 39, 12, 14, 15, 16, 17, 18, 19, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 638 number of broken/clashed sets: 8 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517921 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517921 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517921/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517921 Building REAL300004517922 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517922' /scratch/stefan/7774842/working/building/REAL300004517922 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517922 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517922/0 /scratch/stefan/7774842/working/building/REAL300004517922 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 967) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/967 `/scratch/stefan/7774842/working/3D/967' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)C=CC2=CC=C(C(=O)[O-])N=C2)C=C1C) `REAL300004517922.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517922.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517922/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517922 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C=CC2=CC=C(C(=O)[O-])N=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [44, 32, 61, 61, 16, 4, 1, 1, 1, 1, 1, 1, 16, 29, 29, 61, 61, 126, 126, 126, 126, 126, 126, 126, 126, 61, 61, 61, 61, 61, 61, 61, 61, 4, 4, 1, 1, 1, 65, 65, 126, 126, 126, 61, 61, 61, 61] 201 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 547 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517922 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C=CC2=CC=C(C(=O)[O-])N=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 35, 61, 61, 61, 61, 11, 19, 19, 52, 52, 123, 123, 123, 123, 123, 123, 123, 123, 1, 1, 1, 2, 2, 2, 1, 1, 35, 35, 61, 61, 61, 52, 52, 123, 123, 123, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 43, 25, 26, 27, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46]) total number of confs: 415 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517922 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C=CC2=CC=C(C(=O)[O-])N=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [104, 98, 123, 123, 53, 24, 53, 99, 126, 126, 126, 126, 5, 24, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 123, 123, 123, 123, 123, 123, 123, 123, 99, 99, 126, 126, 126, 5, 5, 1, 1, 1, 123, 123, 123, 123] 201 rigid atoms, others: [40, 41, 42, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 43, 44, 45, 46]) total number of confs: 742 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517922 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517922 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517922/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517922 Building REAL300004517923 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517923' /scratch/stefan/7774842/working/building/REAL300004517923 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517923 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517923/0 /scratch/stefan/7774842/working/building/REAL300004517923 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 968) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/968 `/scratch/stefan/7774842/working/3D/968' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC(C(=O)[O-])=CS2)C=C1C) `REAL300004517923.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517923/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517923 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC(C(=O)[O-])=CS2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 11, 11, 1, 14, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [48, 39, 82, 82, 25, 5, 1, 1, 1, 1, 1, 1, 25, 51, 51, 112, 112, 112, 112, 112, 112, 112, 82, 82, 82, 80, 82, 82, 82, 82, 5, 5, 1, 1, 1, 112, 112, 82, 82, 82, 82] 201 rigid atoms, others: [32, 33, 34, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 35, 36, 37, 38, 39, 40]) total number of confs: 567 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517923 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC(C(=O)[O-])=CS2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 11, 11, 1, 14, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 38, 82, 82, 82, 82, 11, 23, 23, 63, 63, 63, 63, 63, 63, 63, 1, 1, 1, 2, 2, 2, 1, 1, 38, 38, 82, 82, 82, 63, 63, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 22, 23, 24, 28, 29, 37] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 25, 26, 27, 30, 31, 32, 33, 34, 35, 36, 38, 39, 40]) total number of confs: 318 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517923 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC(C(=O)[O-])=CS2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 11, 11, 1, 14, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [50, 45, 63, 63, 25, 11, 25, 66, 112, 112, 112, 112, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 63, 63, 63, 63, 63, 63, 63, 63, 66, 66, 112, 112, 112, 1, 1, 63, 63, 63, 63] 201 rigid atoms, others: [35, 36, 12, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 37, 38, 39, 40]) total number of confs: 519 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517923 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517923 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517923/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517923 Building REAL300004517924 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517924' /scratch/stefan/7774842/working/building/REAL300004517924 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517924 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517924/0 /scratch/stefan/7774842/working/building/REAL300004517924 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 969) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/969 `/scratch/stefan/7774842/working/3D/969' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@@H]2[C@H]3CC[C@H](O3)[C@@H]2C(=O)[O-])C=C1C) `REAL300004517924.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517924 none CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@@H]2[C@H]3CC[C@H](O3)[C@@H]2C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 7, 5, 7, 5, 5, 5, 7, 12, 5, 7, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [17, 9, 27, 27, 9, 3, 1, 1, 1, 1, 1, 1, 9, 14, 14, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 27, 27, 27, 27, 27, 27, 27, 27, 3, 3, 1, 1, 1, 15, 15, 15, 15, 27, 27, 27, 27] 29 rigid atoms, others: [6, 38, 7, 8, 9, 10, 11, 40, 39] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 188 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517924 none CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@@H]2[C@H]3CC[C@H](O3)[C@@H]2C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 7, 5, 7, 5, 5, 5, 7, 12, 5, 7, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 19, 27, 27, 27, 27, 11, 13, 13, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 15, 17, 17, 1, 1, 1, 2, 2, 2, 1, 1, 19, 19, 27, 27, 27, 15, 15, 15, 15, 1, 2, 2, 2] 29 rigid atoms, others: [0, 1, 2, 3, 4, 5, 34, 45, 35, 28, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 46, 47, 48]) total number of confs: 111 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517924 none CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@@H]2[C@H]3CC[C@H](O3)[C@@H]2C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 7, 5, 7, 5, 5, 5, 7, 12, 5, 7, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 29 conformations in input total number of sets (complete confs): 29 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 15, 15, 6, 3, 6, 11, 15, 15, 15, 15, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 15, 15, 15, 15, 15, 15, 15, 15, 11, 11, 15, 15, 15, 1, 1, 1, 1, 15, 15, 15, 15] 29 rigid atoms, others: [41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 46, 47, 48]) total number of confs: 122 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517924 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517924 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517924/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517924 Building REAL300004517925 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517925' /scratch/stefan/7774842/working/building/REAL300004517925 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517925 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517925/0 /scratch/stefan/7774842/working/building/REAL300004517925 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 970) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/970 `/scratch/stefan/7774842/working/3D/970' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=CC3=C(C(=O)[O-])C=CC=C23)C=C1C) `REAL300004517925.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517925 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=CC3=C(C(=O)[O-])C=CC=C23)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [97, 53, 97, 97, 25, 5, 1, 1, 1, 1, 1, 1, 25, 64, 64, 101, 101, 101, 101, 101, 101, 101, 101, 101, 101, 101, 101, 97, 97, 97, 97, 97, 97, 97, 97, 5, 5, 1, 1, 1, 101, 101, 101, 101, 101, 101, 97, 97, 97, 97] 201 rigid atoms, others: [37, 6, 7, 8, 9, 10, 11, 39, 38] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 516 number of broken/clashed sets: 4 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517925 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=CC3=C(C(=O)[O-])C=CC=C23)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 49, 97, 97, 97, 97, 11, 39, 39, 83, 83, 83, 83, 83, 83, 83, 83, 83, 83, 83, 83, 1, 1, 1, 2, 2, 2, 1, 1, 49, 49, 97, 97, 97, 83, 83, 83, 83, 83, 83, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 33, 34, 46, 27, 28, 29] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49]) total number of confs: 411 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517925 none CC1=CC=C(N(CC2=CC=CO2)C(=O)C2=CC=CC3=C(C(=O)[O-])C=CC=C23)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [83, 57, 83, 83, 23, 7, 23, 70, 101, 101, 101, 101, 1, 7, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 1, 83, 83, 83, 83, 83, 83, 83, 83, 70, 70, 101, 101, 101, 1, 1, 1, 1, 1, 1, 83, 83, 83, 83] 201 rigid atoms, others: [40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 20, 23, 24, 25, 26, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 21, 22, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 46, 47, 48, 49]) total number of confs: 522 number of broken/clashed sets: 4 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517925 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517925 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517925/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517925 Building REAL300004517926 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517926' /scratch/stefan/7774842/working/building/REAL300004517926 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517926 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517926/0 /scratch/stefan/7774842/working/building/REAL300004517926 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 971) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/971 `/scratch/stefan/7774842/working/3D/971' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@@]2(C(C)C)C[C@H]2C(=O)[O-])C=C1C) `REAL300004517926.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517926/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517926 none CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@@]2(C(C)C)C[C@H]2C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 5, 5, 5, 5, 5, 7, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 2, 2, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 5, 5] 5 rigid atoms, others: [34, 35, 36, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 15 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517926 none CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@@]2(C(C)C)C[C@H]2C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 5, 5, 5, 5, 5, 7, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 1, 3, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 5, 5, 1, 1, 1, 2, 2, 2, 1, 1, 5, 5, 5, 5, 5, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 2, 2, 2] 5 rigid atoms, others: [0, 1, 2, 3, 4, 5, 46, 24, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49]) total number of confs: 39 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517926 none CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@@]2(C(C)C)C[C@H]2C(=O)[O-])C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 5, 5, 5, 5, 5, 7, 1, 11, 11, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 5 conformations in input total number of sets (complete confs): 5 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 2, 2, 2, 3, 3, 3, 3, 3, 1, 2, 1, 1, 2, 2, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 1, 1, 3, 3, 3, 3] 5 rigid atoms, others: [12, 44, 45, 14, 15, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 46, 47, 48, 49]) total number of confs: 25 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517926 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517926 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517926/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517926 Building REAL300004517927 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517927' /scratch/stefan/7774842/working/building/REAL300004517927 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517927 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517927/0 /scratch/stefan/7774842/working/building/REAL300004517927 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 972) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/972 `/scratch/stefan/7774842/working/3D/972' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)CC2=CC=C(C(=O)[O-])C=C2C)C=C1C) `REAL300004517927.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517927.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517927/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517927 none CC1=CC=C(N(CC2=CC=CO2)C(=O)CC2=CC=C(C(=O)[O-])C=C2C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [29, 15, 45, 45, 15, 3, 1, 1, 1, 1, 1, 1, 15, 23, 23, 67, 105, 105, 105, 105, 105, 105, 105, 105, 105, 45, 45, 45, 45, 45, 45, 45, 45, 3, 3, 1, 1, 1, 67, 67, 105, 105, 105, 105, 105, 105, 45, 45, 45, 45] 201 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 539 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517927 none CC1=CC=C(N(CC2=CC=CO2)C(=O)CC2=CC=C(C(=O)[O-])C=C2C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 33, 45, 45, 45, 45, 11, 15, 15, 49, 96, 96, 95, 96, 96, 96, 96, 96, 96, 1, 1, 1, 2, 2, 2, 1, 1, 33, 33, 45, 45, 45, 49, 49, 96, 96, 96, 96, 96, 96, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 46, 25, 26, 27, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 47, 48, 49]) total number of confs: 381 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517927 none CC1=CC=C(N(CC2=CC=CO2)C(=O)CC2=CC=C(C(=O)[O-])C=C2C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [80, 42, 96, 96, 42, 22, 42, 99, 105, 105, 105, 105, 6, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 96, 96, 96, 96, 96, 96, 96, 96, 99, 99, 105, 105, 105, 6, 6, 1, 1, 1, 2, 2, 2, 96, 96, 96, 96] 201 rigid atoms, others: [40, 41, 42, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 802 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517927 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517927 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517927/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517927 Building REAL300004517928 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517928' /scratch/stefan/7774842/working/building/REAL300004517928 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517928 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517928/0 /scratch/stefan/7774842/working/building/REAL300004517928 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 973) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/973 `/scratch/stefan/7774842/working/3D/973' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)CC2=CC(C(=O)[O-])=CS2)C=C1C) `REAL300004517928.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517928.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517928/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517928 none CC1=CC=C(N(CC2=CC=CO2)C(=O)CC2=CC(C(=O)[O-])=CS2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 1, 1, 1, 1, 11, 11, 1, 14, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [43, 43, 43, 43, 15, 4, 1, 1, 1, 1, 1, 1, 15, 23, 23, 54, 106, 106, 106, 106, 106, 106, 106, 43, 43, 43, 43, 43, 43, 43, 43, 4, 4, 1, 1, 1, 54, 54, 106, 106, 43, 43, 43, 43] 201 rigid atoms, others: [33, 34, 35, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 325 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517928 none CC1=CC=C(N(CC2=CC=CO2)C(=O)CC2=CC(C(=O)[O-])=CS2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 1, 1, 1, 1, 11, 11, 1, 14, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 31, 43, 43, 43, 43, 11, 15, 15, 39, 96, 96, 96, 96, 96, 96, 96, 1, 1, 1, 2, 2, 2, 1, 1, 31, 31, 43, 43, 43, 39, 39, 96, 96, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 40, 23, 24, 25, 29, 30] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37, 38, 39, 41, 42, 43]) total number of confs: 322 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517928 none CC1=CC=C(N(CC2=CC=CO2)C(=O)CC2=CC(C(=O)[O-])=CS2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'S.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 1, 1, 1, 1, 11, 11, 1, 14, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [96, 96, 96, 96, 47, 31, 47, 96, 106, 106, 106, 106, 8, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 96, 96, 96, 96, 96, 96, 96, 96, 96, 96, 106, 106, 106, 8, 8, 1, 1, 96, 96, 96, 96] 201 rigid atoms, others: [38, 39, 14, 15, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 40, 41, 42, 43]) total number of confs: 515 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517928 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517928 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517928/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517928 Building REAL300004517929 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517929' /scratch/stefan/7774842/working/building/REAL300004517929 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517929 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517929/0 /scratch/stefan/7774842/working/building/REAL300004517929 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 974) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/974 `/scratch/stefan/7774842/working/3D/974' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)CC2=CC=C(C(=O)[O-])C(F)=C2)C=C1C) `REAL300004517929.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517929/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517929 none CC1=CC=C(N(CC2=CC=CO2)C(=O)CC2=CC=C(C(=O)[O-])C(F)=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [13, 13, 42, 42, 13, 3, 1, 1, 1, 1, 1, 1, 13, 19, 19, 51, 98, 98, 98, 98, 108, 108, 98, 98, 98, 42, 42, 42, 42, 42, 42, 42, 42, 3, 3, 1, 1, 1, 51, 51, 98, 98, 98, 42, 42, 42, 42] 201 rigid atoms, others: [35, 36, 37, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 537 number of broken/clashed sets: 1 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517929 none CC1=CC=C(N(CC2=CC=CO2)C(=O)CC2=CC=C(C(=O)[O-])C(F)=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 30, 42, 42, 42, 42, 11, 15, 15, 39, 85, 85, 85, 85, 112, 112, 85, 85, 85, 1, 1, 1, 2, 2, 2, 1, 1, 30, 30, 42, 42, 42, 39, 39, 85, 85, 85, 1, 2, 2, 2] 201 rigid atoms, others: [0, 1, 2, 3, 4, 5, 32, 43, 25, 26, 27, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 28, 29, 30, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46]) total number of confs: 444 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517929 none CC1=CC=C(N(CC2=CC=CO2)C(=O)CC2=CC=C(C(=O)[O-])C(F)=C2)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 1, 1, 1, 1, 1, 11, 11, 1, 15, 1, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [35, 35, 85, 85, 35, 23, 35, 85, 98, 98, 98, 98, 7, 23, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 85, 85, 85, 85, 85, 85, 85, 85, 85, 85, 98, 98, 98, 7, 7, 1, 1, 1, 85, 85, 85, 85] 201 rigid atoms, others: [40, 41, 42, 14, 15, 16, 17, 18, 19, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 20, 21, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 43, 44, 45, 46]) total number of confs: 843 number of broken/clashed sets: 1 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517929 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517929 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517929/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517929 Building REAL300004517930 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517930' /scratch/stefan/7774842/working/building/REAL300004517930 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517930 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517930/0 /scratch/stefan/7774842/working/building/REAL300004517930 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 975) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/975 `/scratch/stefan/7774842/working/3D/975' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@H]2[C@@H](C(=O)[O-])C2(C)C)C=C1C) `REAL300004517930.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517930.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517930/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2', 'output.3.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517930 none CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@H]2[C@@H](C(=O)[O-])C2(C)C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 7, 5, 7, 1, 11, 11, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [60, 60, 60, 60, 17, 4, 1, 1, 1, 1, 1, 1, 17, 31, 31, 37, 37, 37, 37, 37, 37, 37, 37, 37, 60, 60, 60, 60, 60, 60, 60, 60, 4, 4, 1, 1, 1, 37, 37, 37, 37, 37, 37, 60, 60, 60, 60] 69 rigid atoms, others: [34, 35, 36, 6, 7, 8, 9, 10, 11] set([0, 1, 2, 3, 4, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 177 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517930 none CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@H]2[C@@H](C(=O)[O-])C2(C)C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 7, 5, 7, 1, 11, 11, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 11, 30, 60, 60, 60, 60, 11, 25, 25, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 2, 2, 2, 1, 1, 30, 30, 60, 60, 60, 29, 29, 29, 29, 29, 29, 1, 2, 2, 2] 69 rigid atoms, others: [0, 1, 2, 3, 4, 5, 43, 24, 25, 26, 30, 31] set([6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 27, 28, 29, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 44, 45, 46]) total number of confs: 230 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.3.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.3.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517930 none CC1=CC=C(N(CC2=CC=CO2)C(=O)[C@H]2[C@@H](C(=O)[O-])C2(C)C)C=C1C NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 1, 1, 1, 12, 1, 11, 5, 7, 5, 7, 1, 11, 11, 5, 5, 5, 1, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 69 conformations in input total number of sets (complete confs): 69 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 29, 29, 8, 3, 8, 20, 37, 37, 37, 37, 1, 3, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29, 20, 20, 37, 37, 37, 2, 2, 2, 2, 2, 2, 29, 29, 29, 29] 69 rigid atoms, others: [12, 14, 15, 16, 17, 18, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 19, 20, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 146 number of broken/clashed sets: 3 ./output.3.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517930 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517930 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517930/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517930 Building REAL300004517931 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517931' /scratch/stefan/7774842/working/building/REAL300004517931 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517931 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517931/0 /scratch/stefan/7774842/working/building/REAL300004517931 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 976) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/976 `/scratch/stefan/7774842/working/3D/976' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC=C(C(=O)[O-])C=C1)C1=CC=CC(Br)=C1) `REAL300004517931.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517931.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517931/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517931 none CCN(C(=O)C1=CC=C(C(=O)[O-])C=C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [21, 11, 1, 11, 39, 39, 43, 43, 41, 42, 43, 43, 43, 43, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 43, 43, 43, 43, 1, 1, 1, 1] 53 rigid atoms, others: [32, 33, 2, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 179 number of broken/clashed sets: 21 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517931 none CCN(C(=O)C1=CC=C(C(=O)[O-])C=C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [21, 12, 4, 1, 4, 1, 1, 1, 1, 1, 2, 2, 1, 1, 12, 43, 43, 31, 43, 43, 43, 21, 21, 21, 21, 21, 1, 1, 1, 1, 43, 43, 43, 43] 53 rigid atoms, others: [3, 5, 6, 7, 8, 9, 12, 13, 26, 27, 28, 29] set([0, 1, 2, 4, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33]) total number of confs: 177 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517931 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517931 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517931/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517931 Building REAL300004517932 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517932' /scratch/stefan/7774842/working/building/REAL300004517932 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517932 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517932/0 /scratch/stefan/7774842/working/building/REAL300004517932 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 977) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/977 `/scratch/stefan/7774842/working/3D/977' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC=CC(OCC(=O)[O-])=C1)C1=CC=CC(Br)=C1) `REAL300004517932.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517932.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517932/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517932 none CCN(C(=O)C1=CC=CC(OCC(=O)[O-])=C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 11, 1, 11, 23, 23, 45, 45, 45, 45, 45, 120, 192, 192, 192, 45, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 45, 45, 45, 192, 192, 45, 1, 1, 1, 1] 201 rigid atoms, others: [2, 35, 36, 37, 34, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 652 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517932 none CCN(C(=O)C1=CC=CC(OCC(=O)[O-])=C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [30, 21, 9, 1, 9, 1, 1, 1, 1, 1, 1, 6, 16, 29, 29, 1, 21, 45, 45, 44, 45, 45, 45, 30, 30, 30, 30, 30, 1, 1, 1, 16, 16, 1, 45, 45, 45, 45] 201 rigid atoms, others: [33, 3, 5, 6, 7, 8, 9, 10, 15, 28, 29, 30] set([0, 1, 2, 4, 11, 12, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 31, 32, 34, 35, 36, 37]) total number of confs: 245 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517932 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517932 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517932/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517932 Building REAL300004517933 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517933' /scratch/stefan/7774842/working/building/REAL300004517933 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517933 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517933/0 /scratch/stefan/7774842/working/building/REAL300004517933 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 978) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/978 `/scratch/stefan/7774842/working/3D/978' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC=CC(C(=O)[O-])=C1)C1=CC=CC(Br)=C1) `REAL300004517933.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517933 none CCN(C(=O)C1=CC=CC(C(=O)[O-])=C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [23, 12, 1, 12, 39, 39, 72, 72, 72, 72, 72, 72, 72, 72, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 72, 72, 72, 72, 1, 1, 1, 1] 90 rigid atoms, others: [32, 33, 2, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 227 number of broken/clashed sets: 27 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517933 none CCN(C(=O)C1=CC=CC(C(=O)[O-])=C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 90 conformations in input total number of sets (complete confs): 90 using faster count positions algorithm for large data unique positions, atoms: [39, 23, 9, 1, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 23, 72, 72, 57, 72, 72, 72, 39, 39, 39, 39, 39, 1, 1, 1, 1, 72, 72, 72, 72] 90 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 13, 26, 27, 28, 29] set([0, 1, 2, 4, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33]) total number of confs: 301 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517933 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517933 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517933/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517933 Building REAL300004517934 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517934' /scratch/stefan/7774842/working/building/REAL300004517934 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517934 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517934/0 /scratch/stefan/7774842/working/building/REAL300004517934 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 979) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/979 `/scratch/stefan/7774842/working/3D/979' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC=C(C(=O)[O-])S1)C1=CC=CC(Br)=C1) `REAL300004517934.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517934/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517934 none CCN(C(=O)C1=CC=C(C(=O)[O-])S1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 14, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [21, 11, 1, 11, 45, 45, 105, 105, 105, 105, 105, 105, 105, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 105, 105, 1, 1, 1, 1] 109 rigid atoms, others: [2, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 270 number of broken/clashed sets: 25 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517934 none CCN(C(=O)C1=CC=C(C(=O)[O-])S1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'S.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 14, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 109 conformations in input total number of sets (complete confs): 109 using faster count positions algorithm for large data unique positions, atoms: [50, 36, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 36, 105, 105, 79, 105, 105, 105, 50, 50, 50, 50, 50, 1, 1, 105, 105, 105, 105] 109 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 11, 12, 25, 26] set([0, 1, 2, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30]) total number of confs: 378 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517934 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517934 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517934/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517934 Building REAL300004517935 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517935' /scratch/stefan/7774842/working/building/REAL300004517935 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517935 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517935/0 /scratch/stefan/7774842/working/building/REAL300004517935 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 980) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/980 `/scratch/stefan/7774842/working/3D/980' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC=CC(C(=O)[O-])=N1)C1=CC=CC(Br)=C1) `REAL300004517935.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517935.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517935/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517935 none CCN(C(=O)C1=CC=CC(C(=O)[O-])=N1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [21, 11, 1, 11, 41, 41, 100, 100, 100, 100, 100, 100, 100, 100, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 100, 100, 100, 1, 1, 1, 1] 120 rigid atoms, others: [32, 2, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 256 number of broken/clashed sets: 45 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517935 none CCN(C(=O)C1=CC=CC(C(=O)[O-])=N1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 120 conformations in input total number of sets (complete confs): 120 using faster count positions algorithm for large data unique positions, atoms: [53, 35, 10, 1, 10, 1, 1, 1, 1, 1, 1, 2, 2, 1, 35, 100, 100, 82, 100, 100, 100, 53, 53, 53, 53, 53, 1, 1, 1, 100, 100, 100, 100] 120 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 13, 26, 27, 28] set([0, 1, 2, 4, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32]) total number of confs: 386 number of broken/clashed sets: 45 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517935 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517935 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517935/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517935 Building REAL300004517936 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517936' /scratch/stefan/7774842/working/building/REAL300004517936 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517936 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517936/0 /scratch/stefan/7774842/working/building/REAL300004517936 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 981) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/981 `/scratch/stefan/7774842/working/3D/981' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)CCC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC(Br)=C1) `REAL300004517936.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517936.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517936/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517936 none CCN(C(=O)CCC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 11, 1, 11, 45, 45, 128, 137, 183, 183, 150, 150, 183, 183, 183, 183, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 128, 128, 137, 137, 183, 183, 183, 183, 1, 1, 1, 1] 201 rigid atoms, others: [2, 36, 37, 38, 39, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 820 number of broken/clashed sets: 49 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517936 none CCN(C(=O)CCC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [114, 88, 36, 8, 36, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 88, 183, 183, 175, 183, 183, 183, 114, 114, 114, 114, 114, 8, 8, 4, 4, 1, 1, 1, 1, 183, 183, 183, 183] 201 rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39]) total number of confs: 603 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517936 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517936 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517936/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517936 Building REAL300004517937 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517937' /scratch/stefan/7774842/working/building/REAL300004517937 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517937 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517937/0 /scratch/stefan/7774842/working/building/REAL300004517937 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 982) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/982 `/scratch/stefan/7774842/working/3D/982' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC=NC(C(=O)[O-])=C1)C1=CC=CC(Br)=C1) `REAL300004517937.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517937.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517937/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517937 none CCN(C(=O)C1=CC=NC(C(=O)[O-])=C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [21, 11, 1, 11, 41, 41, 75, 75, 75, 75, 75, 75, 75, 75, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 75, 75, 75, 1, 1, 1, 1] 93 rigid atoms, others: [32, 2, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 223 number of broken/clashed sets: 25 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517937 none CCN(C(=O)C1=CC=NC(C(=O)[O-])=C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 93 conformations in input total number of sets (complete confs): 93 using faster count positions algorithm for large data unique positions, atoms: [43, 25, 9, 1, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 25, 75, 75, 61, 75, 75, 75, 43, 43, 43, 43, 43, 1, 1, 1, 75, 75, 75, 75] 93 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 13, 26, 27, 28] set([0, 1, 2, 4, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32]) total number of confs: 317 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517937 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517937 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517937/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517937 Building REAL300004517938 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517938' /scratch/stefan/7774842/working/building/REAL300004517938 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517938 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517938/0 /scratch/stefan/7774842/working/building/REAL300004517938 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 983) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/983 `/scratch/stefan/7774842/working/3D/983' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C=CC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC(Br)=C1) `REAL300004517938.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517938.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517938/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517938 none CCN(C(=O)C=CC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [21, 11, 1, 11, 43, 43, 155, 155, 160, 160, 155, 155, 160, 160, 160, 160, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 155, 155, 160, 160, 160, 160, 1, 1, 1, 1] 188 rigid atoms, others: [2, 35, 36, 37, 34, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 510 number of broken/clashed sets: 63 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517938 none CCN(C(=O)C=CC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 188 conformations in input total number of sets (complete confs): 188 using faster count positions algorithm for large data unique positions, atoms: [89, 64, 21, 3, 21, 3, 1, 1, 1, 1, 1, 1, 2, 2, 1, 1, 64, 160, 160, 153, 160, 160, 160, 89, 89, 89, 89, 89, 3, 3, 1, 1, 1, 1, 160, 160, 159, 160] 188 rigid atoms, others: [32, 33, 6, 7, 8, 9, 10, 11, 14, 15, 30, 31] set([0, 1, 2, 3, 4, 5, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 34, 35, 36, 37]) total number of confs: 489 number of broken/clashed sets: 63 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517938 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517938 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517938/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517938 Building REAL300004517939 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517939' /scratch/stefan/7774842/working/building/REAL300004517939 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517939 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517939/0 /scratch/stefan/7774842/working/building/REAL300004517939 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 984) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/984 `/scratch/stefan/7774842/working/3D/984' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC(C(=O)[O-])=CC([N+](=O)[O-])=C1)C1=CC=CC(Br)=C1) `REAL300004517939.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517939.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517939/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517939 none CCN(C(=O)C1=CC(C(=O)[O-])=CC([N+](=O)[O-])=C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [19, 11, 1, 11, 31, 31, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 78, 78, 78, 1, 1, 1, 1] 104 rigid atoms, others: [32, 33, 2, 35, 34, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 201 number of broken/clashed sets: 31 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517939 none CCN(C(=O)C1=CC(C(=O)[O-])=CC([N+](=O)[O-])=C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [44, 26, 9, 1, 9, 1, 1, 1, 1, 2, 2, 1, 1, 1, 2, 2, 1, 26, 78, 78, 68, 78, 78, 78, 44, 44, 44, 44, 44, 1, 1, 1, 78, 78, 74, 78] 104 rigid atoms, others: [3, 5, 6, 7, 8, 11, 12, 13, 16, 29, 30, 31] set([0, 1, 2, 4, 9, 10, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 297 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517939 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517939 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517939/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517939 Building REAL300004517940 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517940' /scratch/stefan/7774842/working/building/REAL300004517940 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517940 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517940/0 /scratch/stefan/7774842/working/building/REAL300004517940 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 985) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/985 `/scratch/stefan/7774842/working/3D/985' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC(C(=O)[O-])=CC([N+](=O)[O-])=C1)C1=CC=CC(Br)=C1) `REAL300004517940.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517940.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517940/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517940 none CCN(C(=O)C1=CC(C(=O)[O-])=CC([N+](=O)[O-])=C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [19, 11, 1, 11, 31, 31, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 78, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 78, 78, 78, 1, 1, 1, 1] 104 rigid atoms, others: [32, 33, 2, 35, 34, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 201 number of broken/clashed sets: 31 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517940 none CCN(C(=O)C1=CC(C(=O)[O-])=CC([N+](=O)[O-])=C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.pl3', 'O.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 11, 11, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 104 conformations in input total number of sets (complete confs): 104 using faster count positions algorithm for large data unique positions, atoms: [44, 26, 9, 1, 9, 1, 1, 1, 1, 2, 2, 1, 1, 1, 2, 2, 1, 26, 78, 78, 68, 78, 78, 78, 44, 44, 44, 44, 44, 1, 1, 1, 78, 78, 74, 78] 104 rigid atoms, others: [3, 5, 6, 7, 8, 11, 12, 13, 16, 29, 30, 31] set([0, 1, 2, 4, 9, 10, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 297 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517940 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517940 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517940/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517940 Building REAL300004517941 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517941' /scratch/stefan/7774842/working/building/REAL300004517941 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517941 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517941/0 /scratch/stefan/7774842/working/building/REAL300004517941 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 986) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/986 `/scratch/stefan/7774842/working/3D/986' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC=C(C(=O)[O-])O1)C1=CC=CC(Br)=C1) `REAL300004517941.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517941.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517941/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517941 none CCN(C(=O)C1=CC=C(C(=O)[O-])O1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [21, 11, 1, 11, 47, 47, 125, 125, 125, 125, 125, 125, 125, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 125, 125, 1, 1, 1, 1] 143 rigid atoms, others: [2, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 287 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517941 none CCN(C(=O)C1=CC=C(C(=O)[O-])O1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [71, 41, 12, 1, 12, 1, 1, 1, 1, 1, 1, 1, 1, 41, 125, 125, 91, 125, 125, 125, 71, 71, 71, 71, 71, 1, 1, 125, 125, 125, 125] 143 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 11, 12, 25, 26] set([0, 1, 2, 4, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30]) total number of confs: 543 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517941 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517941 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517941/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517941 Building REAL300004517942 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517942' /scratch/stefan/7774842/working/building/REAL300004517942 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517942 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517942/0 /scratch/stefan/7774842/working/building/REAL300004517942 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 987) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/987 `/scratch/stefan/7774842/working/3D/987' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)CCC1=CC=CC=C1C(=O)[O-])C1=CC=CC(Br)=C1) `REAL300004517942.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517942.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517942/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517942 none CCN(C(=O)CCC1=CC=CC=C1C(=O)[O-])C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 11, 1, 11, 36, 36, 126, 147, 180, 180, 180, 180, 180, 180, 180, 180, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 126, 126, 147, 147, 180, 180, 180, 180, 1, 1, 1, 1] 201 rigid atoms, others: [2, 36, 37, 38, 39, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 700 number of broken/clashed sets: 32 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517942 none CCN(C(=O)CCC1=CC=CC=C1C(=O)[O-])C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [104, 81, 35, 10, 35, 6, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 79, 180, 180, 164, 180, 180, 180, 104, 104, 104, 104, 104, 10, 10, 6, 6, 1, 1, 1, 1, 180, 180, 180, 180] 201 rigid atoms, others: [32, 33, 34, 35, 6, 7, 8, 9, 10, 11, 12, 13] set([0, 1, 2, 3, 4, 5, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 36, 37, 38, 39]) total number of confs: 612 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517942 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517942 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517942/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517942 Building REAL300004517943 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517943' /scratch/stefan/7774842/working/building/REAL300004517943 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517943 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517943/0 /scratch/stefan/7774842/working/building/REAL300004517943 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 988) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/988 `/scratch/stefan/7774842/working/3D/988' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)CC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC(Br)=C1) `REAL300004517943.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517943.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517943/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517943 none CCN(C(=O)CC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 11, 1, 11, 33, 33, 116, 169, 169, 169, 169, 169, 169, 169, 169, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 116, 116, 169, 169, 169, 169, 1, 1, 1, 1] 201 rigid atoms, others: [33, 2, 35, 36, 34, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 560 number of broken/clashed sets: 52 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517943 none CCN(C(=O)CC1=CC=CC(C(=O)[O-])=C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [103, 77, 30, 7, 30, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 77, 169, 169, 158, 169, 169, 169, 103, 103, 103, 103, 103, 7, 7, 1, 1, 1, 1, 169, 169, 158, 169] 201 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 14, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36]) total number of confs: 568 number of broken/clashed sets: 52 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517943 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517943 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517943/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517943 Building REAL300004517944 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517944' /scratch/stefan/7774842/working/building/REAL300004517944 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517944 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517944/0 /scratch/stefan/7774842/working/building/REAL300004517944 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 989) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/989 `/scratch/stefan/7774842/working/3D/989' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1CCCC(C(=O)[O-])C1)C1=CC=CC(Br)=C1) `REAL300004517944.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517944.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517944/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517944 none CCN(C(=O)C1CCCC(C(=O)[O-])C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [14, 10, 1, 10, 16, 16, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 1, 1, 1, 1] 21 rigid atoms, others: [2, 36, 37, 38, 39, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 77 number of broken/clashed sets: 5 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517944 none CCN(C(=O)C1CCCC(C(=O)[O-])C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 21 conformations in input total number of sets (complete confs): 21 using default count positions algorithm for smaller data unique positions, atoms: [9, 7, 4, 1, 4, 1, 1, 1, 1, 1, 1, 3, 3, 1, 7, 18, 18, 14, 18, 18, 18, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18] 21 rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 10, 13, 35, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 4, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 36, 37, 38, 39]) total number of confs: 73 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517944 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517944 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517944/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517944 Building REAL300004517945 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517945' /scratch/stefan/7774842/working/building/REAL300004517945 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517945 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517945/0 /scratch/stefan/7774842/working/building/REAL300004517945 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 990) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/990 `/scratch/stefan/7774842/working/3D/990' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC=C(C(=O)[O-])N=C1)C1=CC=CC(Br)=C1) `REAL300004517945.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517945.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517945/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517945 none CCN(C(=O)C1=CC=C(C(=O)[O-])N=C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [21, 11, 1, 11, 36, 36, 79, 79, 79, 79, 79, 79, 79, 79, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 79, 79, 79, 1, 1, 1, 1] 95 rigid atoms, others: [32, 2, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 231 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517945 none CCN(C(=O)C1=CC=C(C(=O)[O-])N=C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [39, 23, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 79, 79, 55, 79, 79, 79, 39, 39, 39, 39, 39, 1, 1, 1, 79, 79, 79, 79] 95 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 26, 27, 28] set([0, 1, 2, 4, 32, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31]) total number of confs: 325 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517945 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517945 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517945/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517945 Building REAL300004517946 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517946' /scratch/stefan/7774842/working/building/REAL300004517946 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517946 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517946/0 /scratch/stefan/7774842/working/building/REAL300004517946 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 991) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/991 `/scratch/stefan/7774842/working/3D/991' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC=C(C(=O)[O-])C=N1)C1=CC=CC(Br)=C1) `REAL300004517946.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517946.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517946/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517946 none CCN(C(=O)C1=CC=C(C(=O)[O-])C=N1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [21, 11, 1, 11, 44, 44, 121, 121, 121, 121, 121, 121, 121, 121, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 121, 121, 121, 1, 1, 1, 1] 125 rigid atoms, others: [32, 2, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 276 number of broken/clashed sets: 36 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517946 none CCN(C(=O)C1=CC=C(C(=O)[O-])C=N1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [54, 38, 11, 1, 11, 1, 1, 1, 1, 1, 2, 2, 1, 1, 38, 121, 121, 97, 121, 121, 121, 54, 54, 54, 54, 54, 1, 1, 1, 121, 121, 121, 121] 125 rigid atoms, others: [3, 5, 6, 7, 8, 9, 12, 13, 26, 27, 28] set([0, 1, 2, 4, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32]) total number of confs: 423 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517946 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517946 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517946/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517946 Building REAL300004517947 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517947' /scratch/stefan/7774842/working/building/REAL300004517947 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517947 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517947/0 /scratch/stefan/7774842/working/building/REAL300004517947 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 992) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/992 `/scratch/stefan/7774842/working/3D/992' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)CC(C)(C)CC(=O)[O-])C1=CC=CC(Br)=C1) `REAL300004517947.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517947.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517947/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517947 none CCN(C(=O)CC(C)(C)CC(=O)[O-])C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 11, 1, 11, 27, 27, 49, 115, 115, 115, 193, 197, 197, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 49, 49, 119, 119, 119, 119, 119, 119, 193, 193, 1, 1, 1, 1] 201 rigid atoms, others: [2, 35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 971 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517947 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517947 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517947/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517947 Building REAL300004517948 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517948' /scratch/stefan/7774842/working/building/REAL300004517948 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517948 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517948/0 /scratch/stefan/7774842/working/building/REAL300004517948 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 993) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/993 `/scratch/stefan/7774842/working/3D/993' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC=C(C(=O)[O-])C=C1F)C1=CC=CC(Br)=C1) `REAL300004517948.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517948.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517948/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517948 none CCN(C(=O)C1=CC=C(C(=O)[O-])C=C1F)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 15, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [21, 11, 1, 11, 37, 37, 79, 79, 70, 79, 79, 79, 79, 79, 79, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 79, 79, 79, 1, 1, 1, 1] 96 rigid atoms, others: [32, 33, 2, 15, 16, 17, 18, 19, 20, 21, 30, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 275 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517948 none CCN(C(=O)C1=CC=C(C(=O)[O-])C=C1F)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 15, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [46, 26, 10, 1, 10, 1, 1, 1, 1, 1, 2, 2, 1, 1, 1, 26, 79, 79, 54, 79, 79, 79, 46, 46, 46, 46, 46, 1, 1, 1, 79, 79, 54, 79] 96 rigid atoms, others: [3, 5, 6, 7, 8, 9, 12, 13, 14, 27, 28, 29] set([0, 1, 2, 4, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 32, 33]) total number of confs: 317 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517948 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517948 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517948/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517948 Building REAL300004517949 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517949' /scratch/stefan/7774842/working/building/REAL300004517949 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517949 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517949/0 /scratch/stefan/7774842/working/building/REAL300004517949 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 994) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/994 `/scratch/stefan/7774842/working/3D/994' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CN=C(C(=O)[O-])C=N1)C1=CC=CC(Br)=C1) `REAL300004517949.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517949.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517949/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517949 none CCN(C(=O)C1=CN=C(C(=O)[O-])C=N1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 11, 11, 1, 8, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [21, 11, 1, 11, 42, 42, 111, 111, 111, 111, 111, 111, 111, 111, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 111, 111, 1, 1, 1, 1] 115 rigid atoms, others: [2, 14, 15, 16, 17, 18, 19, 20, 28, 29, 30, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27]) total number of confs: 264 number of broken/clashed sets: 30 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517949 none CCN(C(=O)C1=CN=C(C(=O)[O-])C=N1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 11, 11, 1, 8, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 115 conformations in input total number of sets (complete confs): 115 using faster count positions algorithm for large data unique positions, atoms: [50, 36, 11, 1, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 111, 111, 87, 111, 111, 111, 50, 50, 50, 50, 50, 1, 1, 111, 111, 102, 111] 115 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 26, 27] set([0, 1, 2, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 28, 29, 30, 31]) total number of confs: 371 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517949 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517949 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517949/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517949 Building REAL300004517950 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517950' /scratch/stefan/7774842/working/building/REAL300004517950 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517950 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517950/0 /scratch/stefan/7774842/working/building/REAL300004517950 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 995) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/995 `/scratch/stefan/7774842/working/3D/995' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@H]1CC[C@H](C(=O)[O-])CC1)C1=CC=CC(Br)=C1) `REAL300004517950.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517950.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517950/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517950 none CCN(C(=O)[C@H]1CC[C@H](C(=O)[O-])CC1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 11, 5, 5, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [25, 13, 1, 13, 49, 49, 93, 93, 93, 93, 93, 93, 108, 108, 93, 93, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 93, 93, 93, 93, 93, 93, 93, 93, 1, 1, 1, 1] 108 rigid atoms, others: [2, 36, 37, 38, 39, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 411 number of broken/clashed sets: 37 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517950 none CCN(C(=O)[C@H]1CC[C@H](C(=O)[O-])CC1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 11, 5, 5, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 108 conformations in input total number of sets (complete confs): 108 using faster count positions algorithm for large data unique positions, atoms: [30, 22, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 22, 93, 93, 55, 93, 93, 93, 30, 30, 30, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 93, 93, 93, 93] 108 rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 10, 11, 14, 15, 35, 28, 29, 30, 31] set([0, 1, 2, 4, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 36, 37, 38, 39]) total number of confs: 359 number of broken/clashed sets: 37 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517950 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517950 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517950/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517950 Building REAL300004517951 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517951' /scratch/stefan/7774842/working/building/REAL300004517951 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517951 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517951/0 /scratch/stefan/7774842/working/building/REAL300004517951 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 996) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/996 `/scratch/stefan/7774842/working/3D/996' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1CCC(C(=O)[O-])CC1)C1=CC=CC(Br)=C1) `REAL300004517951.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517951/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517951 none CCN(C(=O)C1CCC(C(=O)[O-])CC1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 11, 5, 5, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [21, 12, 1, 12, 25, 25, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 33, 33, 33, 33, 33, 33, 33, 33, 33, 33, 1, 1, 1, 1] 37 rigid atoms, others: [2, 36, 37, 38, 39, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 147 number of broken/clashed sets: 11 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517951 none CCN(C(=O)C1CCC(C(=O)[O-])CC1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 11, 5, 5, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 37 conformations in input total number of sets (complete confs): 37 using default count positions algorithm for smaller data unique positions, atoms: [13, 11, 6, 1, 6, 1, 1, 1, 1, 1, 3, 3, 1, 1, 11, 33, 33, 25, 33, 33, 33, 13, 13, 13, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 25, 33] 37 rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 12, 13, 35, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 4, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 36, 37, 38, 39]) total number of confs: 103 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517951 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517951 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517951/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517951 Building REAL300004517952 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517952' /scratch/stefan/7774842/working/building/REAL300004517952 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517952 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517952/0 /scratch/stefan/7774842/working/building/REAL300004517952 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 997) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/997 `/scratch/stefan/7774842/working/3D/997' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)CC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC(Br)=C1) `REAL300004517952.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517952/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517952 none CCN(C(=O)CC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [21, 11, 1, 11, 34, 34, 140, 170, 170, 165, 170, 170, 170, 170, 170, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 140, 140, 170, 170, 170, 170, 1, 1, 1, 1] 192 rigid atoms, others: [33, 2, 35, 36, 34, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 628 number of broken/clashed sets: 54 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517952 none CCN(C(=O)CC1=CC=C(C(=O)[O-])C=C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 192 conformations in input total number of sets (complete confs): 192 using faster count positions algorithm for large data unique positions, atoms: [98, 70, 21, 4, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 70, 170, 170, 147, 170, 170, 170, 98, 98, 98, 98, 98, 4, 4, 1, 1, 1, 1, 170, 170, 170, 170] 192 rigid atoms, others: [32, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 29, 30, 31] set([0, 1, 2, 3, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36]) total number of confs: 618 number of broken/clashed sets: 55 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517952 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517952 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517952/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517952 Building REAL300004517953 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517953' /scratch/stefan/7774842/working/building/REAL300004517953 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517953 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517953/0 /scratch/stefan/7774842/working/building/REAL300004517953 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 998) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/998 `/scratch/stefan/7774842/working/3D/998' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)CN1C=C(C(=O)[O-])N=N1)C1=CC=CC(Br)=C1) `REAL300004517953.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517953/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517953 none CCN(C(=O)CN1C=C(C(=O)[O-])N=N1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 11, 11, 8, 8, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 11, 1, 11, 28, 28, 73, 163, 163, 163, 163, 163, 163, 163, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 73, 73, 163, 1, 1, 1, 1] 201 rigid atoms, others: [32, 2, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 439 number of broken/clashed sets: 23 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517953 none CCN(C(=O)CN1C=C(C(=O)[O-])N=N1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 11, 11, 8, 8, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [117, 92, 47, 9, 47, 1, 1, 1, 1, 1, 2, 2, 1, 1, 92, 163, 163, 157, 163, 163, 163, 117, 117, 117, 117, 117, 9, 9, 1, 163, 163, 163, 163] 201 rigid atoms, others: [5, 6, 7, 8, 9, 12, 13, 28] set([0, 1, 2, 3, 4, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32]) total number of confs: 574 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517953 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517953 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517953/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517953 Building REAL300004517954 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517954' /scratch/stefan/7774842/working/building/REAL300004517954 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517954 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517954/0 /scratch/stefan/7774842/working/building/REAL300004517954 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 999) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/999 `/scratch/stefan/7774842/working/3D/999' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC=C(C(=O)[O-])C(C)=N1)C1=CC=CC(Br)=C1) `REAL300004517954.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517954/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517954 none CCN(C(=O)C1=CC=C(C(=O)[O-])C(C)=N1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 5, 8, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 176 conformations in input total number of sets (complete confs): 176 using faster count positions algorithm for large data unique positions, atoms: [25, 13, 1, 13, 52, 52, 150, 150, 150, 150, 162, 162, 150, 150, 150, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 150, 150, 150, 150, 150, 1, 1, 1, 1] 176 rigid atoms, others: [32, 33, 2, 35, 34, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 391 number of broken/clashed sets: 49 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517954 none CCN(C(=O)C1=CC=C(C(=O)[O-])C(C)=N1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.3', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 5, 8, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 176 conformations in input total number of sets (complete confs): 176 using faster count positions algorithm for large data unique positions, atoms: [59, 39, 12, 1, 12, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 39, 150, 150, 86, 150, 150, 150, 59, 59, 59, 59, 59, 1, 1, 2, 2, 2, 150, 150, 96, 150] 176 rigid atoms, others: [3, 5, 6, 7, 8, 9, 12, 13, 14, 27, 28] set([0, 1, 2, 4, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 544 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517954 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517954 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517954/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517954 Building REAL300004517955 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517955' /scratch/stefan/7774842/working/building/REAL300004517955 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517955 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517955/0 /scratch/stefan/7774842/working/building/REAL300004517955 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 1000) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/1000 `/scratch/stefan/7774842/working/3D/1000' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC=C(C(=O)[O-])C=C1)C1=CC=CC(Br)=C1) `REAL300004517955.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517955.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517955/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517955 none CCN(C(=O)C1=CC=C(C(=O)[O-])C=C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [21, 11, 1, 11, 39, 39, 43, 43, 41, 42, 43, 43, 43, 43, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 43, 43, 43, 43, 1, 1, 1, 1] 53 rigid atoms, others: [32, 33, 2, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 179 number of broken/clashed sets: 21 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517955 none CCN(C(=O)C1=CC=C(C(=O)[O-])C=C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 53 conformations in input total number of sets (complete confs): 53 using faster count positions algorithm for large data unique positions, atoms: [21, 12, 4, 1, 4, 1, 1, 1, 1, 1, 2, 2, 1, 1, 12, 43, 43, 31, 43, 43, 43, 21, 21, 21, 21, 21, 1, 1, 1, 1, 43, 43, 43, 43] 53 rigid atoms, others: [3, 5, 6, 7, 8, 9, 12, 13, 26, 27, 28, 29] set([0, 1, 2, 4, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33]) total number of confs: 177 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517955 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517955 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517955/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517955 Building REAL300004517956 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517956' /scratch/stefan/7774842/working/building/REAL300004517956 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517956 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517956/0 /scratch/stefan/7774842/working/building/REAL300004517956 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 1001) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/1001 `/scratch/stefan/7774842/working/3D/1001' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@H]1CC[C@@H](C(=O)[O-])C1)C1=CC=CC(Br)=C1) `REAL300004517956.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517956.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517956/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517956 none CCN(C(=O)[C@H]1CC[C@@H](C(=O)[O-])C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 11, 5, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [21, 11, 1, 11, 37, 37, 64, 64, 64, 64, 64, 64, 68, 68, 64, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 64, 64, 64, 64, 64, 64, 1, 1, 1, 1] 89 rigid atoms, others: [33, 2, 35, 36, 34, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 263 number of broken/clashed sets: 27 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517956 none CCN(C(=O)[C@H]1CC[C@@H](C(=O)[O-])C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 11, 5, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [34, 20, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 20, 64, 64, 48, 64, 64, 64, 34, 34, 34, 34, 34, 1, 1, 1, 1, 1, 1, 64, 64, 64, 64] 89 rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 10, 11, 14, 27, 28, 29, 30, 31] set([0, 1, 2, 4, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 33, 34, 35, 36]) total number of confs: 265 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517956 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517956 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517956/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517956 Building REAL300004517957 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517957' /scratch/stefan/7774842/working/building/REAL300004517957 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517957 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517957/0 /scratch/stefan/7774842/working/building/REAL300004517957 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 1002) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/1002 `/scratch/stefan/7774842/working/3D/1002' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC=CC(CC(=O)[O-])=C1)C1=CC=CC(Br)=C1) `REAL300004517957.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517957.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517957/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517957 none CCN(C(=O)C1=CC=CC(CC(=O)[O-])=C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [23, 12, 1, 12, 45, 45, 108, 108, 77, 108, 108, 168, 170, 170, 108, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 108, 108, 77, 168, 168, 108, 1, 1, 1, 1] 201 rigid atoms, others: [33, 2, 35, 36, 34, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 731 number of broken/clashed sets: 50 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517957 none CCN(C(=O)C1=CC=CC(CC(=O)[O-])=C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [51, 31, 11, 1, 11, 1, 1, 1, 1, 1, 1, 2, 7, 7, 1, 31, 108, 108, 78, 108, 108, 108, 51, 51, 51, 51, 51, 1, 1, 1, 2, 2, 1, 108, 108, 108, 108] 201 rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 10, 14, 27, 28, 29] set([0, 1, 2, 4, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 30, 31, 33, 34, 35, 36]) total number of confs: 445 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517957 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517957 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517957/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517957 Building REAL300004517958 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517958' /scratch/stefan/7774842/working/building/REAL300004517958 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517958 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517958/0 /scratch/stefan/7774842/working/building/REAL300004517958 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 1003) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/1003 `/scratch/stefan/7774842/working/3D/1003' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=C(CC(=O)[O-])OC=C1)C1=CC=CC(Br)=C1) `REAL300004517958.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517958.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517958/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517958 none CCN(C(=O)C1=C(CC(=O)[O-])OC=C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 5, 1, 11, 11, 12, 1, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [21, 11, 1, 11, 31, 31, 70, 70, 74, 82, 82, 70, 70, 70, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 74, 74, 70, 70, 1, 1, 1, 1] 96 rigid atoms, others: [32, 33, 2, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 256 number of broken/clashed sets: 20 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517958 none CCN(C(=O)C1=C(CC(=O)[O-])OC=C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 5, 1, 11, 11, 12, 1, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 96 conformations in input total number of sets (complete confs): 96 using faster count positions algorithm for large data unique positions, atoms: [47, 29, 9, 1, 9, 1, 1, 1, 2, 7, 7, 1, 1, 1, 29, 70, 70, 67, 70, 70, 70, 47, 47, 47, 47, 47, 2, 2, 1, 1, 70, 70, 70, 70] 96 rigid atoms, others: [3, 5, 6, 7, 11, 12, 13, 28, 29] set([0, 1, 2, 4, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33]) total number of confs: 281 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517958 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517958 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517958/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517958 Building REAL300004517959 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517959' /scratch/stefan/7774842/working/building/REAL300004517959 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517959 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517959/0 /scratch/stefan/7774842/working/building/REAL300004517959 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 1004) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/1004 `/scratch/stefan/7774842/working/3D/1004' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=C(CC(=O)[O-])OC=C1C)C1=CC=CC(Br)=C1) `REAL300004517959.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517959.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517959/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517959 none CCN(C(=O)C1=C(CC(=O)[O-])OC=C1C)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 5, 1, 11, 11, 12, 1, 1, 5, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [19, 11, 1, 11, 27, 27, 48, 48, 58, 62, 62, 48, 48, 48, 48, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 58, 58, 48, 48, 48, 48, 1, 1, 1, 1] 68 rigid atoms, others: [33, 2, 35, 36, 34, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 232 number of broken/clashed sets: 21 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517959 none CCN(C(=O)C1=C(CC(=O)[O-])OC=C1C)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.2', 'C.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 5, 1, 11, 11, 12, 1, 1, 5, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 68 conformations in input total number of sets (complete confs): 68 using faster count positions algorithm for large data unique positions, atoms: [26, 18, 6, 1, 6, 1, 1, 1, 3, 7, 7, 1, 1, 1, 1, 18, 48, 48, 44, 48, 48, 48, 26, 26, 26, 26, 26, 3, 3, 1, 2, 2, 2, 48, 48, 45, 48] 68 rigid atoms, others: [3, 5, 6, 7, 11, 12, 13, 14, 29] set([0, 1, 2, 4, 8, 9, 10, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 182 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517959 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517959 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517959/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517959 Building REAL300004517960 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517960' /scratch/stefan/7774842/working/building/REAL300004517960 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517960 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517960/0 /scratch/stefan/7774842/working/building/REAL300004517960 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 1005) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/1005 `/scratch/stefan/7774842/working/3D/1005' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC(C(=O)[O-])=CC=N1)C1=CC=CC(Br)=C1) `REAL300004517960.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517960.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517960/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517960 none CCN(C(=O)C1=CC(C(=O)[O-])=CC=N1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [25, 13, 1, 13, 45, 45, 125, 125, 125, 125, 125, 125, 125, 125, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 125, 125, 125, 1, 1, 1, 1] 153 rigid atoms, others: [32, 2, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 305 number of broken/clashed sets: 46 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517960 none CCN(C(=O)C1=CC(C(=O)[O-])=CC=N1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 11, 11, 1, 1, 8, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 153 conformations in input total number of sets (complete confs): 153 using faster count positions algorithm for large data unique positions, atoms: [61, 37, 10, 1, 10, 1, 1, 1, 1, 2, 2, 1, 1, 1, 37, 125, 125, 98, 125, 125, 125, 61, 61, 61, 61, 61, 1, 1, 1, 125, 125, 122, 125] 153 rigid atoms, others: [3, 5, 6, 7, 8, 11, 12, 13, 26, 27, 28] set([0, 1, 2, 4, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32]) total number of confs: 476 number of broken/clashed sets: 46 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517960 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517960 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517960/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517960 Building REAL300004517961 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517961' /scratch/stefan/7774842/working/building/REAL300004517961 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517961 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517961/0 /scratch/stefan/7774842/working/building/REAL300004517961 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 1006) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/1006 `/scratch/stefan/7774842/working/3D/1006' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)CC1CCC(C(=O)[O-])CC1)C1=CC=CC(Br)=C1) `REAL300004517961.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517961 none CCN(C(=O)CC1CCC(C(=O)[O-])CC1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 5, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 11, 1, 11, 33, 33, 114, 163, 164, 164, 164, 174, 174, 164, 162, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 114, 114, 164, 164, 164, 164, 164, 164, 164, 164, 164, 164, 1, 1, 1, 1] 201 rigid atoms, others: [2, 39, 40, 41, 42, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 707 number of broken/clashed sets: 35 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517961 none CCN(C(=O)CC1CCC(C(=O)[O-])CC1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 5, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [103, 68, 25, 6, 25, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 67, 164, 164, 133, 164, 163, 164, 103, 103, 103, 103, 103, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 164, 164, 164, 164] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 13, 14, 37, 38, 29, 30, 31] set([0, 1, 2, 3, 4, 11, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 39, 40, 41, 42]) total number of confs: 699 number of broken/clashed sets: 35 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517961 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517961 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517961/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517961 Building REAL300004517962 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517962' /scratch/stefan/7774842/working/building/REAL300004517962 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517962 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517962/0 /scratch/stefan/7774842/working/building/REAL300004517962 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 1007) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/1007 `/scratch/stefan/7774842/working/3D/1007' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)CC(C)(C)CC(=O)[O-])C1=CC=CC(Br)=C1) `REAL300004517962.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517962.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517962/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517962 none CCN(C(=O)CC(C)(C)CC(=O)[O-])C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 11, 1, 11, 27, 27, 49, 115, 115, 115, 193, 197, 197, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 49, 49, 119, 119, 119, 119, 119, 119, 193, 193, 1, 1, 1, 1] 201 rigid atoms, others: [2, 35, 36, 37, 38, 13, 14, 15, 16, 17, 18, 19] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 971 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517962 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517962 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517962/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517962 Building REAL300004517963 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517963' /scratch/stefan/7774842/working/building/REAL300004517963 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517963 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517963/0 /scratch/stefan/7774842/working/building/REAL300004517963 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 1008) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/1008 `/scratch/stefan/7774842/working/3D/1008' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)CCCC(=O)[O-])C1=CC=CC(Br)=C1) `REAL300004517963.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517963.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517963/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517963 none CCN(C(=O)CCCC(=O)[O-])C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 11, 1, 11, 27, 27, 89, 107, 171, 177, 177, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 89, 89, 117, 117, 168, 168, 1, 1, 1, 1] 201 rigid atoms, others: [32, 2, 11, 12, 13, 14, 15, 16, 17, 29, 30, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 906 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517963 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517963 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517963/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517963 Building REAL300004517964 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517964' /scratch/stefan/7774842/working/building/REAL300004517964 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517964 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517964/0 /scratch/stefan/7774842/working/building/REAL300004517964 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 1009) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/1009 `/scratch/stefan/7774842/working/3D/1009' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)CC(C)CC(=O)[O-])C1=CC=CC(Br)=C1) `REAL300004517964.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517964.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517964/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517964 none CCN(C(=O)CC(C)CC(=O)[O-])C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 11, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 11, 1, 11, 34, 34, 96, 135, 135, 191, 192, 192, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 96, 96, 135, 135, 135, 135, 191, 191, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 2, 34, 12, 13, 14, 15, 16, 17, 18, 35] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 918 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517964 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517964 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517964/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517964 Building REAL300004517965 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517965' /scratch/stefan/7774842/working/building/REAL300004517965 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517965 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517965/0 /scratch/stefan/7774842/working/building/REAL300004517965 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 1010) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/1010 `/scratch/stefan/7774842/working/3D/1010' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC=NC2=C(C(=O)[O-])C=NN21)C1=CC=CC(Br)=C1) `REAL300004517965.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517965.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517965/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517965 none CCN(C(=O)C1=CC=NC2=C(C(=O)[O-])C=NN21)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 8, 8, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [21, 11, 1, 11, 39, 39, 85, 85, 85, 85, 85, 85, 89, 89, 85, 85, 85, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 85, 85, 85, 1, 1, 1, 1] 127 rigid atoms, others: [32, 33, 2, 35, 34, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 249 number of broken/clashed sets: 34 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517965 none CCN(C(=O)C1=CC=NC2=C(C(=O)[O-])C=NN21)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 11, 11, 1, 8, 8, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 127 conformations in input total number of sets (complete confs): 127 using faster count positions algorithm for large data unique positions, atoms: [43, 25, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 1, 25, 85, 85, 61, 85, 85, 85, 43, 43, 43, 43, 43, 1, 1, 1, 85, 85, 84, 85] 127 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 11, 14, 15, 16, 29, 30, 31] set([0, 1, 2, 4, 12, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 32, 33, 34, 35]) total number of confs: 379 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517965 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517965 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517965/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517965 Building REAL300004517966 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517966' /scratch/stefan/7774842/working/building/REAL300004517966 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517966 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517966/0 /scratch/stefan/7774842/working/building/REAL300004517966 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 1011) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/1011 `/scratch/stefan/7774842/working/3D/1011' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=NOC(C(=O)[O-])=C1)C1=CC=CC(Br)=C1) `REAL300004517966.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517966.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517966/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517966 none CCN(C(=O)C1=NOC(C(=O)[O-])=C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 8, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [21, 11, 1, 11, 39, 39, 130, 130, 130, 130, 130, 130, 130, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 130, 1, 1, 1, 1] 146 rigid atoms, others: [2, 13, 14, 15, 16, 17, 18, 19, 26, 27, 28, 29] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25]) total number of confs: 282 number of broken/clashed sets: 36 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517966 none CCN(C(=O)C1=NOC(C(=O)[O-])=C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 8, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 146 conformations in input total number of sets (complete confs): 146 using faster count positions algorithm for large data unique positions, atoms: [69, 45, 12, 1, 12, 1, 1, 1, 1, 1, 2, 2, 1, 45, 130, 130, 111, 130, 130, 130, 69, 69, 69, 69, 69, 1, 130, 130, 130, 130] 146 rigid atoms, others: [3, 5, 6, 7, 8, 9, 12, 25] set([0, 1, 2, 4, 10, 11, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 26, 27, 28, 29]) total number of confs: 474 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517966 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517966 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517966/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517966 Building REAL300004517967 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517967' /scratch/stefan/7774842/working/building/REAL300004517967 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517967 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517967/0 /scratch/stefan/7774842/working/building/REAL300004517967 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 1012) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/1012 `/scratch/stefan/7774842/working/3D/1012' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=C(C)OC(C(=O)[O-])=C1)C1=CC=CC(Br)=C1) `REAL300004517967.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517967.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517967/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517967 none CCN(C(=O)C1=C(C)OC(C(=O)[O-])=C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 5, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [25, 13, 1, 13, 47, 47, 104, 104, 104, 104, 104, 104, 104, 104, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 104, 104, 104, 104, 1, 1, 1, 1] 110 rigid atoms, others: [32, 33, 2, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 279 number of broken/clashed sets: 25 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517967 none CCN(C(=O)C1=C(C)OC(C(=O)[O-])=C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 5, 12, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [47, 33, 10, 1, 10, 1, 1, 1, 1, 1, 1, 2, 2, 1, 33, 104, 104, 87, 104, 104, 104, 47, 47, 47, 47, 47, 2, 2, 2, 1, 104, 104, 87, 104] 110 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 13, 29] set([0, 1, 2, 4, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33]) total number of confs: 330 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517967 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517967 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517967/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517967 Building REAL300004517968 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517968' /scratch/stefan/7774842/working/building/REAL300004517968 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517968 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517968/0 /scratch/stefan/7774842/working/building/REAL300004517968 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 1013) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/1013 `/scratch/stefan/7774842/working/3D/1013' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC(C)=C(C(=O)[O-])O1)C1=CC=CC(Br)=C1) `REAL300004517968.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517968.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517968/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517968 none CCN(C(=O)C1=CC(C)=C(C(=O)[O-])O1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 5, 1, 1, 11, 11, 12, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 11, 1, 11, 45, 45, 155, 155, 155, 155, 155, 181, 181, 155, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 155, 155, 155, 155, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 2, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 422 number of broken/clashed sets: 49 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517968 none CCN(C(=O)C1=CC(C)=C(C(=O)[O-])O1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 5, 1, 1, 11, 11, 12, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [73, 47, 12, 1, 12, 1, 1, 1, 1, 1, 1, 2, 2, 1, 47, 155, 155, 100, 155, 155, 155, 73, 73, 73, 73, 73, 1, 2, 2, 2, 155, 155, 151, 155] 201 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 13, 26] set([0, 1, 2, 4, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 642 number of broken/clashed sets: 49 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517968 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517968 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517968/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517968 Building REAL300004517969 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517969' /scratch/stefan/7774842/working/building/REAL300004517969 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517969 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517969/0 /scratch/stefan/7774842/working/building/REAL300004517969 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 1014) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/1014 `/scratch/stefan/7774842/working/3D/1014' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)CN1C=C(C(=O)[O-])C=N1)C1=CC=CC(Br)=C1) `REAL300004517969.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517969/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517969 none CCN(C(=O)CN1C=C(C(=O)[O-])C=N1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 11, 11, 1, 8, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 11, 1, 11, 27, 27, 73, 180, 180, 180, 180, 180, 180, 180, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 73, 73, 180, 180, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 2, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 452 number of broken/clashed sets: 15 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517969 none CCN(C(=O)CN1C=C(C(=O)[O-])C=N1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 11, 11, 1, 8, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [115, 92, 43, 9, 43, 1, 1, 1, 1, 1, 1, 1, 1, 1, 92, 180, 180, 163, 180, 180, 180, 115, 115, 115, 115, 115, 9, 9, 1, 1, 180, 180, 163, 180] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 11, 12, 13, 28, 29] set([0, 1, 2, 3, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33]) total number of confs: 609 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517969 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517969 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517969/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517969 Building REAL300004517970 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517970' /scratch/stefan/7774842/working/building/REAL300004517970 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517970 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517970/0 /scratch/stefan/7774842/working/building/REAL300004517970 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 1015) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/1015 `/scratch/stefan/7774842/working/3D/1015' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC=C(C=CC(=O)[O-])O1)C1=CC=CC(Br)=C1) `REAL300004517970.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517970.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517970/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517970 none CCN(C(=O)C1=CC=C(C=CC(=O)[O-])O1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 11, 1, 11, 33, 33, 89, 89, 89, 89, 193, 193, 195, 195, 89, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 89, 89, 193, 193, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 2, 34, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 555 number of broken/clashed sets: 28 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517970 none CCN(C(=O)C1=CC=C(C=CC(=O)[O-])O1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [47, 32, 10, 1, 10, 1, 1, 1, 1, 1, 12, 12, 22, 22, 1, 32, 89, 89, 71, 89, 89, 89, 47, 47, 47, 47, 47, 1, 1, 12, 12, 89, 89, 71, 89] 201 rigid atoms, others: [3, 5, 6, 7, 8, 9, 14, 27, 28] set([0, 1, 2, 4, 10, 11, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34]) total number of confs: 357 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517970 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517970 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517970/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517970 Building REAL300004517971 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517971' /scratch/stefan/7774842/working/building/REAL300004517971 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517971 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517971/0 /scratch/stefan/7774842/working/building/REAL300004517971 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 1016) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/1016 `/scratch/stefan/7774842/working/3D/1016' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC=C(OCC(=O)[O-])C=C1)C1=CC=CC(Br)=C1) `REAL300004517971.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517971/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517971 none CCN(C(=O)C1=CC=C(OCC(=O)[O-])C=C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 11, 1, 11, 24, 24, 28, 28, 26, 26, 88, 186, 186, 186, 28, 28, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 28, 28, 186, 186, 28, 28, 1, 1, 1, 1] 201 rigid atoms, others: [2, 35, 36, 37, 34, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 699 number of broken/clashed sets: 28 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517971 none CCN(C(=O)C1=CC=C(OCC(=O)[O-])C=C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [18, 12, 5, 1, 5, 1, 1, 1, 1, 1, 6, 16, 24, 24, 1, 1, 12, 28, 28, 28, 28, 28, 28, 18, 18, 18, 18, 18, 1, 1, 16, 16, 1, 1, 28, 28, 28, 28] 201 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 14, 15, 28, 29] set([0, 1, 2, 4, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 34, 35, 36, 37]) total number of confs: 169 number of broken/clashed sets: 28 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517971 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517971 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517971/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517971 Building REAL300004517972 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517972' /scratch/stefan/7774842/working/building/REAL300004517972 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517972 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517972/0 /scratch/stefan/7774842/working/building/REAL300004517972 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 1017) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/1017 `/scratch/stefan/7774842/working/3D/1017' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)CCSCC(=O)[O-])C1=CC=CC(Br)=C1) `REAL300004517972.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517972.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517972/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517972 none CCN(C(=O)CCSCC(=O)[O-])C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'S.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 14, 5, 1, 11, 11, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [17, 11, 1, 11, 20, 20, 72, 82, 168, 193, 193, 193, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 72, 72, 82, 82, 193, 193, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 2, 12, 13, 14, 15, 16, 17, 18, 30, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 659 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517972 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517972 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517972/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517972 Building REAL300004517973 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517973' /scratch/stefan/7774842/working/building/REAL300004517973 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517973 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517973/0 /scratch/stefan/7774842/working/building/REAL300004517973 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 1018) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/1018 `/scratch/stefan/7774842/working/3D/1018' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC=C(C(=O)[O-])C=N1)C1=CC=CC(Br)=C1) `REAL300004517973.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517973.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517973/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517973 none CCN(C(=O)C1=CC=C(C(=O)[O-])C=N1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [21, 11, 1, 11, 44, 44, 121, 121, 121, 121, 121, 121, 121, 121, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 121, 121, 121, 1, 1, 1, 1] 125 rigid atoms, others: [32, 2, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 276 number of broken/clashed sets: 36 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517973 none CCN(C(=O)C1=CC=C(C(=O)[O-])C=N1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 11, 1, 8, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 125 conformations in input total number of sets (complete confs): 125 using faster count positions algorithm for large data unique positions, atoms: [54, 38, 11, 1, 11, 1, 1, 1, 1, 1, 2, 2, 1, 1, 38, 121, 121, 97, 121, 121, 121, 54, 54, 54, 54, 54, 1, 1, 1, 121, 121, 121, 121] 125 rigid atoms, others: [3, 5, 6, 7, 8, 9, 12, 13, 26, 27, 28] set([0, 1, 2, 4, 10, 11, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32]) total number of confs: 423 number of broken/clashed sets: 36 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517973 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517973 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517973/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517973 Building REAL300004517974 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517974' /scratch/stefan/7774842/working/building/REAL300004517974 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517974 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517974/0 /scratch/stefan/7774842/working/building/REAL300004517974 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 1019) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/1019 `/scratch/stefan/7774842/working/3D/1019' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)COCC(=O)[O-])C1=CC=CC(Br)=C1) `REAL300004517974.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517974/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517974 none CCN(C(=O)COCC(=O)[O-])C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 1, 11, 11, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 3, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 11, 1, 11, 30, 30, 106, 176, 192, 194, 194, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 106, 106, 192, 192, 1, 1, 1, 1] 201 rigid atoms, others: [2, 11, 12, 13, 14, 15, 16, 17, 27, 28, 29, 30] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 648 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517974 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517974 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517974/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517974 Building REAL300004517975 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517975' /scratch/stefan/7774842/working/building/REAL300004517975 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517975 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517975/0 /scratch/stefan/7774842/working/building/REAL300004517975 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 1020) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/1020 `/scratch/stefan/7774842/working/3D/1020' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC(C(=O)[O-])=NN1C)C1=CC=CC(Br)=C1) `REAL300004517975.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517975 none CCN(C(=O)C1=CC(C(=O)[O-])=NN1C)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 11, 11, 8, 8, 5, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [25, 13, 1, 13, 49, 49, 104, 104, 104, 104, 104, 104, 104, 104, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 104, 104, 104, 104, 1, 1, 1, 1] 110 rigid atoms, others: [32, 33, 2, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 285 number of broken/clashed sets: 25 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517975 none CCN(C(=O)C1=CC(C(=O)[O-])=NN1C)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 11, 11, 8, 8, 5, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 110 conformations in input total number of sets (complete confs): 110 using faster count positions algorithm for large data unique positions, atoms: [46, 31, 9, 1, 9, 1, 1, 1, 1, 2, 2, 1, 1, 1, 31, 104, 104, 86, 104, 104, 104, 46, 46, 46, 46, 46, 1, 2, 2, 2, 104, 104, 104, 104] 110 rigid atoms, others: [3, 5, 6, 7, 8, 11, 12, 13, 26] set([0, 1, 2, 4, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 372 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517975 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517975 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517975/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517975 Building REAL300004517976 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517976' /scratch/stefan/7774842/working/building/REAL300004517976 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517976 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517976/0 /scratch/stefan/7774842/working/building/REAL300004517976 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 1021) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/1021 `/scratch/stefan/7774842/working/3D/1021' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@H]1C[C@@H](C)[C@H](C(=O)[O-])O1)C1=CC=CC(Br)=C1) `REAL300004517976.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517976.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517976/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517976 none CCN(C(=O)[C@H]1C[C@@H](C)[C@H](C(=O)[O-])O1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 7, 1, 11, 11, 12, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [25, 13, 1, 13, 53, 53, 109, 109, 109, 109, 109, 109, 109, 109, 123, 123, 109, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 109, 109, 109, 109, 109, 1, 1, 1, 1] 140 rigid atoms, others: [34, 35, 36, 37, 2, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 435 number of broken/clashed sets: 42 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517976 none CCN(C(=O)[C@H]1C[C@@H](C)[C@H](C(=O)[O-])O1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 7, 1, 11, 11, 12, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 140 conformations in input total number of sets (complete confs): 140 using faster count positions algorithm for large data unique positions, atoms: [45, 29, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 29, 109, 109, 61, 109, 109, 109, 45, 45, 45, 45, 45, 1, 1, 2, 2, 2, 109, 109, 109, 109] 140 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 16, 29, 30] set([0, 1, 2, 4, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 486 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517976 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517976 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517976/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517976 Building REAL300004517977 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517977' /scratch/stefan/7774842/working/building/REAL300004517977 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517977 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517977/0 /scratch/stefan/7774842/working/building/REAL300004517977 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 1022) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/1022 `/scratch/stefan/7774842/working/3D/1022' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC=C(CC(=O)[O-])C=C1)C1=CC=CC(Br)=C1) `REAL300004517977.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517977.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517977/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517977 none CCN(C(=O)C1=CC=C(CC(=O)[O-])C=C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [21, 11, 1, 11, 45, 45, 55, 55, 49, 52, 81, 81, 81, 55, 55, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 55, 55, 81, 81, 55, 55, 1, 1, 1, 1] 101 rigid atoms, others: [33, 2, 35, 36, 34, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 374 number of broken/clashed sets: 33 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517977 none CCN(C(=O)C1=CC=C(CC(=O)[O-])C=C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 101 conformations in input total number of sets (complete confs): 101 using faster count positions algorithm for large data unique positions, atoms: [29, 16, 6, 1, 6, 1, 1, 1, 1, 1, 3, 6, 6, 1, 1, 16, 55, 55, 37, 55, 55, 55, 29, 29, 29, 29, 29, 1, 1, 3, 3, 1, 1, 55, 55, 53, 55] 101 rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 13, 14, 27, 28, 31] set([0, 1, 2, 4, 10, 11, 12, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 33, 34, 35, 36]) total number of confs: 255 number of broken/clashed sets: 33 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517977 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517977 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517977/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517977 Building REAL300004517978 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517978' /scratch/stefan/7774842/working/building/REAL300004517978 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517978 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517978/0 /scratch/stefan/7774842/working/building/REAL300004517978 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 1023) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/1023 `/scratch/stefan/7774842/working/3D/1023' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC=C(C=CC(=O)[O-])C=C1)C1=CC=CC(Br)=C1) `REAL300004517978.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517978.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517978/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517978 none CCN(C(=O)C1=CC=C(C=CC(=O)[O-])C=C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [21, 11, 1, 11, 47, 47, 73, 73, 56, 73, 137, 137, 150, 150, 73, 73, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 73, 73, 137, 137, 73, 73, 1, 1, 1, 1] 168 rigid atoms, others: [2, 35, 36, 37, 34, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 583 number of broken/clashed sets: 42 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517978 none CCN(C(=O)C1=CC=C(C=CC(=O)[O-])C=C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 168 conformations in input total number of sets (complete confs): 168 using faster count positions algorithm for large data unique positions, atoms: [27, 15, 6, 1, 6, 1, 1, 1, 1, 1, 5, 5, 19, 19, 1, 1, 15, 73, 73, 37, 73, 73, 73, 27, 27, 27, 27, 27, 1, 1, 5, 5, 1, 1, 73, 73, 73, 73] 168 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 14, 15, 28, 29] set([0, 1, 2, 4, 10, 11, 12, 13, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 34, 35, 36, 37]) total number of confs: 371 number of broken/clashed sets: 42 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517978 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517978 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517978/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517978 Building REAL300004517979 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517979' /scratch/stefan/7774842/working/building/REAL300004517979 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517979 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517979/0 /scratch/stefan/7774842/working/building/REAL300004517979 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 1024) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/1024 `/scratch/stefan/7774842/working/3D/1024' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C=CC1=CC(C(=O)[O-])=CO1)C1=CC=CC(Br)=C1) `REAL300004517979.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517979.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517979/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517979 none CCN(C(=O)C=CC1=CC(C(=O)[O-])=CO1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [20, 11, 1, 11, 35, 35, 119, 119, 198, 198, 198, 198, 198, 198, 198, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 119, 119, 198, 198, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 2, 34, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 497 number of broken/clashed sets: 29 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517979 none CCN(C(=O)C=CC1=CC(C(=O)[O-])=CO1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 11, 1, 12, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [114, 96, 47, 12, 47, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 96, 198, 198, 182, 198, 198, 198, 114, 114, 114, 114, 114, 12, 12, 1, 1, 198, 198, 187, 198] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 29, 30] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34]) total number of confs: 593 number of broken/clashed sets: 29 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517979 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517979 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517979/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517979 Building REAL300004517980 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517980' /scratch/stefan/7774842/working/building/REAL300004517980 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517980 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517980/0 /scratch/stefan/7774842/working/building/REAL300004517980 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 1025) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/1025 `/scratch/stefan/7774842/working/3D/1025' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)COCC1=C(C(=O)[O-])N=CO1)C1=CC=CC(Br)=C1) `REAL300004517980.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517980.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517980/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517980 none CCN(C(=O)COCC1=C(C(=O)[O-])N=CO1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 11, 11, 8, 1, 12, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [9, 7, 1, 7, 11, 11, 41, 87, 156, 189, 189, 189, 189, 189, 189, 189, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 41, 41, 156, 156, 189, 1, 1, 1, 1] 201 rigid atoms, others: [33, 2, 35, 36, 34, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 666 number of broken/clashed sets: 0 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517980 none CCN(C(=O)COCC1=C(C(=O)[O-])N=CO1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 12, 5, 1, 1, 1, 11, 11, 8, 1, 12, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 2, 2, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [148, 130, 112, 52, 112, 22, 6, 1, 1, 1, 1, 2, 2, 1, 1, 1, 130, 189, 189, 175, 189, 189, 189, 148, 148, 148, 148, 148, 52, 52, 6, 6, 1, 189, 189, 189, 189] 201 rigid atoms, others: [32, 7, 8, 9, 10, 13, 14, 15] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 33, 34, 35, 36]) total number of confs: 697 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517980 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517980 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517980/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517980 Building REAL300004517981 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517981' /scratch/stefan/7774842/working/building/REAL300004517981 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517981 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517981/0 /scratch/stefan/7774842/working/building/REAL300004517981 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 1026) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/1026 `/scratch/stefan/7774842/working/3D/1026' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C=CC1=CC=C(C(=O)[O-])O1)C1=CC=CC(Br)=C1) `REAL300004517981.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517981.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517981/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517981 none CCN(C(=O)C=CC1=CC=C(C(=O)[O-])O1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 11, 1, 11, 39, 39, 134, 134, 191, 191, 191, 191, 191, 191, 191, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 134, 134, 191, 191, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 2, 34, 15, 16, 17, 18, 19, 20, 21, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 502 number of broken/clashed sets: 44 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517981 none CCN(C(=O)C=CC1=CC=C(C(=O)[O-])O1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 1, 1, 11, 11, 12, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [123, 101, 48, 12, 48, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 101, 191, 191, 174, 191, 191, 191, 123, 123, 123, 123, 123, 12, 12, 1, 1, 191, 191, 191, 191] 201 rigid atoms, others: [6, 7, 8, 9, 10, 11, 12, 13, 14, 29, 30] set([0, 1, 2, 3, 4, 5, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 31, 32, 33, 34]) total number of confs: 625 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517981 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517981 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517981/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517981 Building REAL300004517982 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517982' /scratch/stefan/7774842/working/building/REAL300004517982 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517982 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517982/0 /scratch/stefan/7774842/working/building/REAL300004517982 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 1027) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/1027 `/scratch/stefan/7774842/working/3D/1027' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@H]1CC[C@@H](C(=O)[O-])C1)C1=CC=CC(Br)=C1) `REAL300004517982.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517982/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517982 none CCN(C(=O)[C@H]1CC[C@@H](C(=O)[O-])C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 11, 5, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [21, 11, 1, 11, 37, 37, 64, 64, 64, 64, 64, 64, 68, 68, 64, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 64, 64, 64, 64, 64, 64, 1, 1, 1, 1] 89 rigid atoms, others: [33, 2, 35, 36, 34, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 263 number of broken/clashed sets: 27 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517982 none CCN(C(=O)[C@H]1CC[C@@H](C(=O)[O-])C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 11, 5, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 89 conformations in input total number of sets (complete confs): 89 using faster count positions algorithm for large data unique positions, atoms: [34, 20, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 20, 64, 64, 48, 64, 64, 64, 34, 34, 34, 34, 34, 1, 1, 1, 1, 1, 1, 64, 64, 64, 64] 89 rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 10, 11, 14, 27, 28, 29, 30, 31] set([0, 1, 2, 4, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 33, 34, 35, 36]) total number of confs: 265 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517982 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517982 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517982/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517982 Building REAL300004517983 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517983' /scratch/stefan/7774842/working/building/REAL300004517983 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517983 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517983/0 /scratch/stefan/7774842/working/building/REAL300004517983 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 1028) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/1028 `/scratch/stefan/7774842/working/3D/1028' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC=C(C)C(C(=O)[O-])=C1)C1=CC=CC(Br)=C1) `REAL300004517983.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517983.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517983/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517983 none CCN(C(=O)C1=CC=C(C)C(C(=O)[O-])=C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [21, 11, 1, 11, 45, 45, 85, 85, 85, 85, 85, 85, 85, 85, 85, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 85, 85, 85, 85, 85, 85, 1, 1, 1, 1] 99 rigid atoms, others: [33, 2, 35, 36, 34, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]) total number of confs: 240 number of broken/clashed sets: 34 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517983 none CCN(C(=O)C1=CC=C(C)C(C(=O)[O-])=C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 5, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 99 conformations in input total number of sets (complete confs): 99 using faster count positions algorithm for large data unique positions, atoms: [40, 25, 9, 1, 9, 1, 1, 1, 1, 1, 1, 1, 2, 2, 1, 25, 85, 85, 62, 85, 85, 85, 40, 40, 40, 40, 40, 1, 1, 2, 2, 2, 1, 85, 85, 65, 85] 99 rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 10, 11, 14, 27, 28] set([0, 1, 2, 4, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 33, 34, 35, 36]) total number of confs: 309 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517983 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517983 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517983/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517983 Building REAL300004517984 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517984' /scratch/stefan/7774842/working/building/REAL300004517984 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517984 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517984/0 /scratch/stefan/7774842/working/building/REAL300004517984 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 1029) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/1029 `/scratch/stefan/7774842/working/3D/1029' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CN=CC(C(=O)[O-])=C1)C1=CC=CC(Br)=C1) `REAL300004517984.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517984.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517984/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517984 none CCN(C(=O)C1=CN=CC(C(=O)[O-])=C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [21, 11, 1, 11, 42, 42, 76, 76, 76, 76, 76, 76, 76, 76, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 76, 76, 76, 1, 1, 1, 1] 95 rigid atoms, others: [32, 2, 14, 15, 16, 17, 18, 19, 20, 29, 30, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 225 number of broken/clashed sets: 26 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517984 none CCN(C(=O)C1=CN=CC(C(=O)[O-])=C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 11, 11, 1, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 95 conformations in input total number of sets (complete confs): 95 using faster count positions algorithm for large data unique positions, atoms: [43, 25, 9, 1, 9, 1, 1, 1, 1, 1, 1, 2, 2, 1, 25, 76, 76, 60, 76, 76, 76, 43, 43, 43, 43, 43, 1, 1, 1, 76, 76, 66, 76] 95 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 13, 26, 27, 28] set([0, 1, 2, 4, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 29, 30, 31, 32]) total number of confs: 303 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517984 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517984 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517984/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517984 Building REAL300004517985 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517985' /scratch/stefan/7774842/working/building/REAL300004517985 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517985 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517985/0 /scratch/stefan/7774842/working/building/REAL300004517985 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 1030) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/1030 `/scratch/stefan/7774842/working/3D/1030' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=CC(C(=O)[O-])=CN=C1C)C1=CC=CC(Br)=C1) `REAL300004517985.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517985.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517985/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517985 none CCN(C(=O)C1=CC(C(=O)[O-])=CN=C1C)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 11, 11, 1, 8, 1, 5, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [22, 12, 1, 12, 38, 38, 62, 62, 62, 62, 62, 62, 62, 62, 62, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22, 62, 62, 62, 62, 62, 1, 1, 1, 1] 86 rigid atoms, others: [32, 33, 2, 35, 34, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 205 number of broken/clashed sets: 21 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517985 none CCN(C(=O)C1=CC(C(=O)[O-])=CN=C1C)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 1, 1, 11, 11, 1, 8, 1, 5, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 86 conformations in input total number of sets (complete confs): 86 using faster count positions algorithm for large data unique positions, atoms: [34, 22, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 62, 62, 58, 62, 62, 62, 34, 34, 34, 34, 34, 1, 1, 2, 2, 2, 62, 62, 62, 62] 86 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 27, 28] set([0, 1, 2, 4, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 211 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517985 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517985 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517985/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517985 Building REAL300004517986 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517986' /scratch/stefan/7774842/working/building/REAL300004517986 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517986 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517986/0 /scratch/stefan/7774842/working/building/REAL300004517986 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 1031) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/1031 `/scratch/stefan/7774842/working/3D/1031' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)CN1C=CC(C(=O)[O-])=N1)C1=CC=CC(Br)=C1) `REAL300004517986.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517986.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517986/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517986 none CCN(C(=O)CN1C=CC(C(=O)[O-])=N1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 11, 1, 11, 32, 32, 78, 172, 172, 172, 172, 172, 172, 172, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 78, 78, 172, 172, 1, 1, 1, 1] 201 rigid atoms, others: [32, 33, 2, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 491 number of broken/clashed sets: 25 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517986 none CCN(C(=O)CN1C=CC(C(=O)[O-])=N1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [104, 76, 39, 9, 39, 1, 1, 1, 1, 1, 1, 2, 2, 1, 76, 172, 172, 172, 172, 172, 172, 104, 104, 104, 104, 104, 9, 9, 1, 1, 172, 172, 172, 172] 201 rigid atoms, others: [5, 6, 7, 8, 9, 10, 13, 28, 29] set([0, 1, 2, 3, 4, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 30, 31, 32, 33]) total number of confs: 534 number of broken/clashed sets: 25 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517986 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517986 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517986/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517986 Building REAL300004517987 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517987' /scratch/stefan/7774842/working/building/REAL300004517987 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517987 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517987/0 /scratch/stefan/7774842/working/building/REAL300004517987 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 1032) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/1032 `/scratch/stefan/7774842/working/3D/1032' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)CCCN1C=CC(C(=O)[O-])=N1)C1=CC=CC(Br)=C1) `REAL300004517987.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517987/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517987 none CCN(C(=O)CCCN1C=CC(C(=O)[O-])=N1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 11, 1, 11, 25, 25, 73, 91, 125, 181, 181, 181, 181, 181, 181, 181, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 73, 73, 97, 97, 123, 123, 181, 181, 1, 1, 1, 1] 201 rigid atoms, others: [2, 36, 37, 38, 39, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 731 number of broken/clashed sets: 20 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517987 none CCN(C(=O)CCCN1C=CC(C(=O)[O-])=N1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'N.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 1, 11, 11, 8, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [147, 115, 65, 27, 65, 13, 7, 1, 1, 1, 1, 1, 1, 2, 2, 1, 115, 181, 181, 165, 181, 181, 181, 147, 147, 147, 147, 147, 27, 27, 13, 13, 7, 7, 1, 1, 181, 181, 181, 181] 201 rigid atoms, others: [34, 35, 7, 8, 9, 10, 11, 12, 15] set([0, 1, 2, 3, 4, 5, 6, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 36, 37, 38, 39]) total number of confs: 787 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517987 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517987 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517987/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517987 Building REAL300004517988 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517988' /scratch/stefan/7774842/working/building/REAL300004517988 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517988 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517988/0 /scratch/stefan/7774842/working/building/REAL300004517988 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 1033) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/1033 `/scratch/stefan/7774842/working/3D/1033' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@H]1CC[C@H]1C(=O)[O-])C1=CC=CC(Br)=C1) `REAL300004517988.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517988.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517988/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517988 none CCN(C(=O)[C@H]1CC[C@H]1C(=O)[O-])C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 11, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [19, 11, 1, 11, 20, 20, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 26, 26, 26, 26, 1, 1, 1, 1] 32 rigid atoms, others: [32, 33, 2, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 129 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517988 none CCN(C(=O)[C@H]1CC[C@H]1C(=O)[O-])C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 11, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [13, 9, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 26, 26, 19, 26, 26, 26, 13, 13, 13, 13, 13, 1, 1, 1, 1, 26, 26, 26, 26] 32 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28, 29] set([0, 1, 2, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33]) total number of confs: 107 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517988 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517988 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517988/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517988 Building REAL300004517989 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517989' /scratch/stefan/7774842/working/building/REAL300004517989 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517989 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517989/0 /scratch/stefan/7774842/working/building/REAL300004517989 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 1034) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/1034 `/scratch/stefan/7774842/working/3D/1034' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@H]1CC[C@@H](CCC(=O)[O-])O1)C1=CC=CC(Br)=C1) `REAL300004517989.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517989.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517989/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517989 none CCN(C(=O)[C@H]1CC[C@@H](CCC(=O)[O-])O1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 5, 5, 1, 11, 11, 12, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [21, 11, 1, 11, 34, 34, 80, 80, 80, 80, 80, 80, 156, 183, 183, 183, 80, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 80, 80, 80, 80, 156, 156, 183, 183, 1, 1, 1, 1] 201 rigid atoms, others: [2, 37, 38, 39, 40, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 812 number of broken/clashed sets: 26 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517989 none CCN(C(=O)[C@H]1CC[C@@H](CCC(=O)[O-])O1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 5, 5, 1, 11, 11, 12, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [39, 26, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 6, 12, 20, 20, 1, 26, 80, 80, 57, 80, 80, 80, 39, 39, 39, 39, 39, 1, 1, 1, 1, 6, 6, 12, 12, 80, 80, 58, 80] 201 rigid atoms, others: [32, 3, 5, 6, 7, 8, 9, 10, 11, 16, 29, 30, 31] set([0, 1, 2, 4, 12, 13, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 364 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517989 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517989 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517989/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517989 Building REAL300004517990 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517990' /scratch/stefan/7774842/working/building/REAL300004517990 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517990 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517990/0 /scratch/stefan/7774842/working/building/REAL300004517990 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 1035) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/1035 `/scratch/stefan/7774842/working/3D/1035' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)CC[C@@H]1C[C@H](C(=O)[O-])CO1)C1=CC=CC(Br)=C1) `REAL300004517990.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517990/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517990 none CCN(C(=O)CC[C@@H]1C[C@H](C(=O)[O-])CO1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 7, 1, 11, 11, 5, 12, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 11, 1, 11, 22, 22, 76, 91, 183, 183, 183, 183, 183, 183, 183, 183, 183, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 76, 76, 97, 97, 183, 183, 183, 183, 1, 1, 1, 1] 201 rigid atoms, others: [2, 37, 38, 39, 40, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 728 number of broken/clashed sets: 12 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517990 none CCN(C(=O)CC[C@@H]1C[C@H](C(=O)[O-])CO1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 7, 5, 5, 7, 1, 11, 11, 5, 12, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [120, 98, 56, 13, 56, 7, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 1, 97, 183, 183, 166, 183, 183, 183, 120, 120, 120, 120, 120, 13, 13, 7, 7, 1, 1, 1, 1, 183, 183, 183, 183] 201 rigid atoms, others: [33, 34, 35, 36, 6, 7, 8, 9, 10, 11, 12, 15, 16] set([0, 1, 2, 3, 4, 5, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 37, 38, 39, 40]) total number of confs: 664 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517990 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517990 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517990/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517990 Building REAL300004517991 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517991' /scratch/stefan/7774842/working/building/REAL300004517991 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517991 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517991/0 /scratch/stefan/7774842/working/building/REAL300004517991 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 1036) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/1036 `/scratch/stefan/7774842/working/3D/1036' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@H]1CC[C@H]1C(=O)[O-])C1=CC=CC(Br)=C1) `REAL300004517991.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517991.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517991/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517991 none CCN(C(=O)[C@H]1CC[C@H]1C(=O)[O-])C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 11, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [19, 11, 1, 11, 20, 20, 26, 26, 26, 26, 26, 26, 26, 26, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 26, 26, 26, 26, 1, 1, 1, 1] 32 rigid atoms, others: [32, 33, 2, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 129 number of broken/clashed sets: 16 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517991 none CCN(C(=O)[C@H]1CC[C@H]1C(=O)[O-])C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 11, 11, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 32 conformations in input total number of sets (complete confs): 32 using default count positions algorithm for smaller data unique positions, atoms: [13, 9, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 3, 3, 9, 26, 26, 19, 26, 26, 26, 13, 13, 13, 13, 13, 1, 1, 1, 1, 26, 26, 26, 26] 32 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 11, 26, 27, 28, 29] set([0, 1, 2, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 31, 32, 33]) total number of confs: 107 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517991 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517991 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517991/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517991 Building REAL300004517992 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517992' /scratch/stefan/7774842/working/building/REAL300004517992 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517992 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517992/0 /scratch/stefan/7774842/working/building/REAL300004517992 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 1037) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/1037 `/scratch/stefan/7774842/working/3D/1037' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@H]1C[C@H]1C(=O)[O-])C1=CC=CC(Br)=C1) `REAL300004517992.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517992/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517992 none CCN(C(=O)[C@H]1C[C@H]1C(=O)[O-])C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 11, 11, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [17, 9, 1, 9, 22, 22, 28, 28, 28, 28, 28, 28, 28, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 28, 28, 1, 1, 1, 1] 33 rigid atoms, others: [2, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 131 number of broken/clashed sets: 10 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517992 none CCN(C(=O)[C@H]1C[C@H]1C(=O)[O-])C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 11, 11, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 33 conformations in input total number of sets (complete confs): 33 using default count positions algorithm for smaller data unique positions, atoms: [13, 10, 5, 1, 5, 1, 1, 1, 1, 1, 1, 3, 3, 10, 28, 28, 28, 28, 28, 28, 13, 13, 13, 13, 13, 1, 1, 28, 28, 28, 28] 33 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25, 26] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30]) total number of confs: 76 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517992 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517992 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517992/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517992 Building REAL300004517993 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517993' /scratch/stefan/7774842/working/building/REAL300004517993 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517993 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517993/0 /scratch/stefan/7774842/working/building/REAL300004517993 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 1038) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/1038 `/scratch/stefan/7774842/working/3D/1038' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1=C(C)C=C(C(=O)[O-])O1)C1=CC=CC(Br)=C1) `REAL300004517993.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517993.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517993/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517993 none CCN(C(=O)C1=C(C)C=C(C(=O)[O-])O1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 5, 1, 1, 1, 11, 11, 12, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [23, 12, 1, 12, 51, 51, 133, 133, 133, 133, 133, 133, 133, 133, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23, 133, 133, 133, 133, 1, 1, 1, 1] 143 rigid atoms, others: [32, 33, 2, 14, 15, 16, 17, 18, 19, 20, 30, 31] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29]) total number of confs: 313 number of broken/clashed sets: 39 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517993 none CCN(C(=O)C1=C(C)C=C(C(=O)[O-])O1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.co2', 'O.co2', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 1, 1, 5, 1, 1, 1, 11, 11, 12, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 143 conformations in input total number of sets (complete confs): 143 using faster count positions algorithm for large data unique positions, atoms: [63, 41, 10, 1, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 133, 133, 99, 133, 133, 133, 63, 63, 63, 63, 63, 2, 2, 2, 1, 133, 133, 120, 133] 143 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 29] set([0, 1, 2, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32, 33]) total number of confs: 491 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517993 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517993 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517993/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517993 Building REAL300004517994 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517994' /scratch/stefan/7774842/working/building/REAL300004517994 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517994 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517994/0 /scratch/stefan/7774842/working/building/REAL300004517994 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 1039) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/1039 `/scratch/stefan/7774842/working/3D/1039' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@H]1C2C=CC(CC2)[C@@H]1C(=O)[O-])C1=CC=CC(Br)=C1) `REAL300004517994.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517994.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517994/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517994 none CCN(C(=O)[C@@H]1C2C=CC(CC2)[C@@H]1C(=O)[O-])C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 5, 1, 1, 5, 5, 5, 5, 7, 1, 11, 11, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [12, 10, 1, 10, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 14, 14, 14, 14, 14, 14, 14, 14, 1, 1, 1, 1] 15 rigid atoms, others: [2, 38, 39, 40, 41, 18, 19, 20, 21, 22, 23, 24] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 49 number of broken/clashed sets: 3 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517994 none CCN(C(=O)[C@@H]1C2C=CC(CC2)[C@@H]1C(=O)[O-])C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 5, 1, 1, 5, 5, 5, 5, 7, 1, 11, 11, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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: [7, 6, 3, 1, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 14, 14, 13, 14, 14, 14, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14] 15 rigid atoms, others: [32, 33, 34, 3, 36, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 35, 37, 30, 31] set([0, 1, 2, 4, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 38, 39, 40, 41]) total number of confs: 44 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517994 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517994 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517994/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517994 Building REAL300004517995 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517995' /scratch/stefan/7774842/working/building/REAL300004517995 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517995 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517995/0 /scratch/stefan/7774842/working/building/REAL300004517995 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 1040) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/1040 `/scratch/stefan/7774842/working/3D/1040' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C(=O)[O-])C(=O)N(CC)C1=CC=CC(Br)=C1) `REAL300004517995.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517995.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517995/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517995 none CCC(C(=O)[O-])C(=O)N(CC)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 11, 1, 11, 8, 5, 5, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 2, 2, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 85 conformations in input total number of sets (complete confs): 85 using faster count positions algorithm for large data unique positions, atoms: [71, 48, 36, 48, 53, 53, 11, 36, 1, 11, 21, 1, 1, 1, 1, 1, 1, 1, 71, 71, 71, 71, 71, 48, 21, 21, 21, 21, 21, 1, 1, 1, 1] 85 rigid atoms, others: [32, 8, 11, 12, 13, 14, 15, 16, 17, 29, 30, 31] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 10, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28]) total number of confs: 371 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517995 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517995 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517995/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517995 Building REAL300004517996 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517996' /scratch/stefan/7774842/working/building/REAL300004517996 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517996 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517996/0 /scratch/stefan/7774842/working/building/REAL300004517996 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 1041) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/1041 `/scratch/stefan/7774842/working/3D/1041' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C(C(=O)[O-])C(C)C)C1=CC=CC(Br)=C1) `REAL300004517996.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517996/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.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: REAL300004517996 none CCN(C(=O)C(C(=O)[O-])C(C)C)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 11, 11, 5, 5, 5, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 11, 1, 11, 26, 26, 37, 39, 39, 37, 44, 44, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18, 18, 37, 44, 44, 44, 44, 44, 44, 44, 1, 1, 1, 1] 50 rigid atoms, others: [32, 33, 2, 34, 12, 13, 14, 15, 16, 17, 18, 35] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31]) total number of confs: 218 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517996 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517996 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517996/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517996 Building REAL300004517997 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517997' /scratch/stefan/7774842/working/building/REAL300004517997 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517997 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517997/0 /scratch/stefan/7774842/working/building/REAL300004517997 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 1042) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/1042 `/scratch/stefan/7774842/working/3D/1042' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@H]1CCCC[C@H]1C(=O)[O-])C1=CC=CC(Br)=C1) `REAL300004517997.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517997/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517997 none CCN(C(=O)[C@H]1CCCC[C@H]1C(=O)[O-])C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 5, 7, 1, 11, 11, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [20, 11, 1, 11, 22, 22, 29, 29, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20, 20, 29, 29, 29, 29, 29, 29, 29, 29, 1, 1, 1, 1] 38 rigid atoms, others: [2, 36, 37, 38, 39, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 139 number of broken/clashed sets: 13 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517997 none CCN(C(=O)[C@H]1CCCC[C@H]1C(=O)[O-])C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 5, 7, 1, 11, 11, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 38 conformations in input total number of sets (complete confs): 38 using default count positions algorithm for smaller data unique positions, atoms: [16, 11, 4, 1, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 11, 29, 29, 25, 29, 29, 29, 16, 16, 16, 16, 16, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29] 38 rigid atoms, others: [32, 33, 34, 3, 5, 6, 7, 8, 9, 10, 11, 12, 13, 35, 28, 29, 30, 31] set([0, 1, 2, 4, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 36, 37, 38, 39]) total number of confs: 113 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517997 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517997 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517997/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517997 Building REAL300004517998 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517998' /scratch/stefan/7774842/working/building/REAL300004517998 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 3 protomers extracted for REAL300004517998 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517998/0 /scratch/stefan/7774842/working/building/REAL300004517998 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 1043) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/1043 `/scratch/stefan/7774842/working/3D/1043' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C[N@@H+]1CCCC(C(=O)[O-])C1)C1=CC=CC(Br)=C1) `REAL300004517998.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517998/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517998 none CCN(C(=O)C[N@@H+]1CCCC(C(=O)[O-])C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 1, 11, 11, 5, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [21, 11, 1, 11, 28, 28, 71, 105, 105, 105, 105, 105, 105, 117, 117, 105, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 71, 71, 105, 105, 105, 105, 105, 105, 105, 105, 105, 1, 1, 1, 1] 139 rigid atoms, others: [2, 39, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 489 number of broken/clashed sets: 26 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517998 none CCN(C(=O)C[N@@H+]1CCCC(C(=O)[O-])C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 1, 11, 11, 5, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 139 conformations in input total number of sets (complete confs): 139 using faster count positions algorithm for large data unique positions, atoms: [69, 46, 20, 5, 20, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 46, 105, 105, 85, 105, 105, 105, 69, 69, 69, 69, 69, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 105, 105, 94, 105] 139 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 12, 15, 38, 37, 30, 31] set([0, 1, 2, 3, 4, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42]) total number of confs: 440 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517998 /scratch/stefan/7774842/working /scratch/stefan/7774842 mkdir: created directory `1' /scratch/stefan/7774842/working/building/REAL300004517998/1 /scratch/stefan/7774842/working/building/REAL300004517998 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 1 (index: 1044) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/1044 `/scratch/stefan/7774842/working/3D/1044' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C[N@H+]1CCCC(C(=O)[O-])C1)C1=CC=CC(Br)=C1) `REAL300004517998.mol2' -> `1.mol2' `temp.mol2' -> `REAL300004517998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517998/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517998 none CCN(C(=O)C[N@H+]1CCCC(C(=O)[O-])C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 1, 11, 11, 5, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [21, 11, 1, 11, 27, 27, 66, 95, 95, 95, 95, 95, 95, 114, 114, 95, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 66, 66, 95, 95, 95, 95, 95, 95, 95, 95, 95, 1, 1, 1, 1] 135 rigid atoms, others: [2, 39, 40, 41, 42, 16, 17, 18, 19, 20, 21, 22] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 488 number of broken/clashed sets: 135 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517998 none CCN(C(=O)C[N@H+]1CCCC(C(=O)[O-])C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.4', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 9, 6, 5, 5, 5, 5, 1, 11, 11, 5, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 1, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 135 conformations in input total number of sets (complete confs): 135 using faster count positions algorithm for large data unique positions, atoms: [61, 40, 18, 5, 18, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 40, 95, 95, 69, 95, 95, 95, 61, 61, 61, 61, 61, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 95, 95, 71, 95] 135 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 12, 15, 38, 37, 30, 31] set([0, 1, 2, 3, 4, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42]) total number of confs: 409 number of broken/clashed sets: 135 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517998 /scratch/stefan/7774842/working /scratch/stefan/7774842 mkdir: created directory `2' /scratch/stefan/7774842/working/building/REAL300004517998/2 /scratch/stefan/7774842/working/building/REAL300004517998 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 2 (index: 1045) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/1045 `/scratch/stefan/7774842/working/3D/1045' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)CN1CCCC(C(=O)[O-])C1)C1=CC=CC(Br)=C1) `REAL300004517998.mol2' -> `2.mol2' `temp.mol2' -> `REAL300004517998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517998/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517998 none CCN(C(=O)CN1CCCC(C(=O)[O-])C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 1, 11, 11, 5, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [19, 11, 1, 11, 29, 29, 98, 163, 163, 163, 163, 163, 171, 171, 163, 1, 1, 1, 1, 1, 1, 1, 19, 19, 19, 19, 19, 98, 98, 163, 163, 163, 163, 163, 163, 163, 163, 163, 1, 1, 1, 1] 201 rigid atoms, others: [2, 38, 39, 40, 41, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 548 number of broken/clashed sets: 18 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517998 none CCN(C(=O)CN1CCCC(C(=O)[O-])C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 5, 1, 11, 11, 5, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 201 conformations in input total number of sets (complete confs): 201 using faster count positions algorithm for large data unique positions, atoms: [101, 74, 30, 10, 30, 1, 1, 1, 1, 1, 1, 1, 3, 3, 1, 72, 163, 163, 140, 163, 162, 163, 101, 101, 101, 101, 101, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 163, 163, 150, 163] 201 rigid atoms, others: [32, 33, 34, 35, 36, 5, 6, 7, 8, 9, 10, 11, 14, 37, 29, 30, 31] set([0, 1, 2, 3, 4, 12, 13, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 38, 39, 40, 41]) total number of confs: 619 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517998 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517998 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 2: /scratch/stefan/7774842/working/building/REAL300004517998/2.* 1: /scratch/stefan/7774842/working/building/REAL300004517998/1.* 0: /scratch/stefan/7774842/working/building/REAL300004517998/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517998 Building REAL300004517999 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004517999' /scratch/stefan/7774842/working/building/REAL300004517999 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004517999 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004517999/0 /scratch/stefan/7774842/working/building/REAL300004517999 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 1046) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/1046 `/scratch/stefan/7774842/working/3D/1046' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)[C@@H]1C[C@H]1C(=O)[O-])C1=CC=CC(Br)=C1) `REAL300004517999.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004517999.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004517999/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517999 none CCN(C(=O)[C@@H]1C[C@H]1C(=O)[O-])C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 11, 11, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [25, 13, 1, 13, 53, 53, 131, 131, 131, 131, 131, 145, 145, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 131, 131, 1, 1, 1, 1] 165 rigid atoms, others: [2, 13, 14, 15, 16, 17, 18, 19, 27, 28, 29, 30] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 20, 21, 22, 23, 24, 25, 26]) total number of confs: 501 number of broken/clashed sets: 56 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004517999 none CCN(C(=O)[C@@H]1C[C@H]1C(=O)[O-])C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.co2', 'O.co2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 1, 11, 11, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 165 conformations in input total number of sets (complete confs): 165 using faster count positions algorithm for large data unique positions, atoms: [55, 34, 8, 1, 8, 1, 1, 1, 1, 1, 1, 3, 3, 34, 131, 131, 81, 131, 131, 131, 55, 55, 55, 55, 55, 1, 1, 131, 131, 131, 131] 165 rigid atoms, others: [3, 5, 6, 7, 8, 9, 10, 25, 26] set([0, 1, 2, 4, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 27, 28, 29, 30]) total number of confs: 524 number of broken/clashed sets: 56 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004517999 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004517999 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004517999/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004517999 Building REAL300004518000 mkdir: created directory `/scratch/stefan/7774842/working/building/REAL300004518000' /scratch/stefan/7774842/working/building/REAL300004518000 /scratch/stefan/7774842/working /scratch/stefan/7774842 Extracting previously generated protomers and correcting pH mod types 1 protomers extracted for REAL300004518000 mkdir: created directory `0' /scratch/stefan/7774842/working/building/REAL300004518000/0 /scratch/stefan/7774842/working/building/REAL300004518000 /scratch/stefan/7774842/working /scratch/stefan/7774842 Protomer 0 (index: 1047) Found valid previously generated 3D confromation in /scratch/stefan/7774842/working/3D/1047 `/scratch/stefan/7774842/working/3D/1047' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(C(=O)C1CC2(CC2C(=O)[O-])C1)C1=CC=CC(Br)=C1) `REAL300004518000.mol2' -> `0.mol2' `temp.mol2' -> `REAL300004518000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/stefan/7774842/working/building/REAL300004518000/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' WARNING:root:Setting energy window to 12 and max confs to 200 ('energy: ', 12.0) ('conf: ', 200) ['output.1.db2in.mol2', 'output.2.db2in.mol2'] verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.2.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.2.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004518000 none CCN(C(=O)C1CC2(CC2C(=O)[O-])C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 190 conformations in input total number of sets (complete confs): 190 using faster count positions algorithm for large data unique positions, atoms: [24, 13, 1, 13, 51, 51, 145, 145, 145, 145, 145, 171, 171, 145, 1, 1, 1, 1, 1, 1, 1, 24, 24, 24, 24, 24, 145, 145, 145, 145, 145, 145, 145, 145, 1, 1, 1, 1] 190 rigid atoms, others: [2, 35, 36, 37, 34, 14, 15, 16, 17, 18, 19, 20] set([0, 1, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33]) total number of confs: 565 number of broken/clashed sets: 72 ./output.2.db2in.mol2.db2.gz file written out Cleaning up verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/home/rstein/zzz.github/DOCK/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': False, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} names: REAL300004518000 none CCN(C(=O)C1CC2(CC2C(=O)[O-])C1)C1=CC=CC(Br)=C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.co2', 'O.co2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'Br', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 5, 5, 5, 5, 1, 11, 11, 5, 1, 1, 1, 1, 1, 17, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 2, 2, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 190 conformations in input total number of sets (complete confs): 190 using faster count positions algorithm for large data unique positions, atoms: [58, 35, 8, 1, 8, 1, 1, 1, 1, 1, 1, 3, 3, 1, 35, 145, 145, 95, 145, 145, 145, 58, 58, 58, 58, 58, 1, 1, 1, 1, 1, 1, 1, 1, 145, 145, 145, 145] 190 rigid atoms, others: [32, 33, 3, 5, 6, 7, 8, 9, 10, 13, 26, 27, 28, 29, 30, 31] set([0, 1, 2, 4, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 34, 35, 36, 37]) total number of confs: 595 number of broken/clashed sets: 72 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/stefan/7774842/working/building/REAL300004518000 /scratch/stefan/7774842/working /scratch/stefan/7774842 Finished preparing REAL300004518000 Recording results /scratch/stefan/7774842/working /scratch/stefan/7774842 Appending to /scratch/stefan/7774842/finished/xaaaatx.* 0: /scratch/stefan/7774842/working/building/REAL300004518000/0.* Removing working files in /scratch/stefan/7774842/working/building/REAL300004518000 /scratch/stefan/7774842 Compressing combined databse files /scratch/stefan/7774842/finished/xaaaatx.db2.gz /scratch/stefan/7774842/finished/xaaaatx.solv.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/stefan/7774842/finished) ======================================================= Finalizing... removed `/scratch/stefan/7774842/working/3D/1048' removed directory: `/scratch/stefan/7774842/working/3D' `/scratch/stefan/7774842/working/protonate' -> `/scratch/stefan/7774842/archive' `/scratch/stefan/7774842/working/input-smiles.ism' -> `/scratch/stefan/7774842/archive/input-smiles.ism' rmdir: removing directory, `/scratch/stefan/7774842/working/building' rmdir: removing directory, `/scratch/stefan/7774842/working' ls: No match. ls: No match.